Starting phenix.real_space_refine
on Wed Mar  4 12:03:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xoh_33348/03_2026/7xoh_33348.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      60      5.16       5
     C    8484      2.51       5
     N    2336      2.21       5
     O    2640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13524
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "A"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "C"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "D"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 3.06, per 1000 atoms: 0.23
  Number of scatterers: 13524
  At special positions: 0
  Unit cell: (84.53, 146.59, 84.53, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       4     15.00
     O    2640      8.00
     N    2336      7.00
     C    8484      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 426.3 milliseconds
  

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3208

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 20 sheets defined
      37.4% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 45 through 58
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.869A  pdb=" N   VAL B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ARG B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 109
      removed outlier: 3.929A  pdb=" N   ARG B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.506A  pdb=" N   VAL B 131 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 160
    Processing helix  chain 'B' and resid 161 through 168
      removed outlier: 3.768A  pdb=" N   ILE B 165 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
      removed outlier: 3.512A  pdb=" N   ARG B 191 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR B 192 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 262
      removed outlier: 3.519A  pdb=" N   SER B 251 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 281
      removed outlier: 3.924A  pdb=" N   GLY B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.655A  pdb=" N   MET B 302 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER B 303 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 334
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 390 through 395
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 422 through 431
    Processing helix  chain 'B' and resid 450 through 458
    Processing helix  chain 'A' and resid 6 through 10
      removed outlier: 3.753A  pdb=" N   LEU A  10 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 58
    Processing helix  chain 'A' and resid 74 through 87
      removed outlier: 4.127A  pdb=" N   GLY A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ARG A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 109
      removed outlier: 3.653A  pdb=" N   ARG A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 109 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 139
      removed outlier: 3.580A  pdb=" N   VAL A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 161 through 170
      removed outlier: 3.680A  pdb=" N   THR A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.792A  pdb=" N   GLY A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 262
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.827A  pdb=" N   GLY A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 314
      removed outlier: 3.883A  pdb=" N   TYR A 314 " --> pdb=" O   TRP A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 352 through 364
    Processing helix  chain 'A' and resid 392 through 397
      removed outlier: 3.874A  pdb=" N   PHE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU A 397 " --> pdb=" O   SER A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 397'
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 422 through 431
      removed outlier: 3.695A  pdb=" N   ALA A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 44 through 58
      removed outlier: 3.697A  pdb=" N   LYS C  50 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 87
      removed outlier: 3.855A  pdb=" N   VAL C  77 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY C  78 " --> pdb=" O   ASN C  74 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ARG C  86 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 109
      removed outlier: 3.893A  pdb=" N   ARG C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 139
      removed outlier: 3.506A  pdb=" N   VAL C 131 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 160
    Processing helix  chain 'C' and resid 161 through 168
      removed outlier: 3.646A  pdb=" N   ILE C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 196
    Processing helix  chain 'C' and resid 247 through 262
      removed outlier: 3.561A  pdb=" N   SER C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 281
      removed outlier: 3.902A  pdb=" N   GLY C 271 " --> pdb=" O   GLY C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 303
      removed outlier: 3.671A  pdb=" N   MET C 302 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER C 303 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 299 through 303'
    Processing helix  chain 'C' and resid 329 through 334
    Processing helix  chain 'C' and resid 352 through 362
    Processing helix  chain 'C' and resid 390 through 395
    Processing helix  chain 'C' and resid 405 through 409
    Processing helix  chain 'C' and resid 422 through 430
    Processing helix  chain 'C' and resid 450 through 458
      removed outlier: 3.511A  pdb=" N   GLY C 455 " --> pdb=" O   TYR C 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 10
      removed outlier: 3.749A  pdb=" N   LEU D  10 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 58
      removed outlier: 3.802A  pdb=" N   LYS D  50 " --> pdb=" O   ARG D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 87
      removed outlier: 4.422A  pdb=" N   GLY D  78 " --> pdb=" O   ASN D  74 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG D  86 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 109
      removed outlier: 3.647A  pdb=" N   ARG D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 139
      removed outlier: 3.577A  pdb=" N   VAL D 131 " --> pdb=" O   SER D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 160
    Processing helix  chain 'D' and resid 161 through 170
      removed outlier: 3.704A  pdb=" N   THR D 169 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 196
    Processing helix  chain 'D' and resid 247 through 262
    Processing helix  chain 'D' and resid 267 through 281
      removed outlier: 3.756A  pdb=" N   GLY D 271 " --> pdb=" O   GLY D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 334
    Processing helix  chain 'D' and resid 352 through 364
      removed outlier: 3.685A  pdb=" N   TYR D 363 " --> pdb=" O   ILE D 359 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 409
    Processing helix  chain 'D' and resid 422 through 430
      removed outlier: 3.918A  pdb=" N   ALA D 426 " --> pdb=" O   LEU D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 450 through 458
      removed outlier: 3.591A  pdb=" N   GLY D 455 " --> pdb=" O   TYR D 451 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19
      removed outlier: 4.778A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 116
      removed outlier: 6.536A  pdb=" N   CYS B  90 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   VAL B 114 " --> pdb=" O   CYS B  90 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE B  92 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   CYS B 116 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   CYS B  94 " --> pdb=" O   CYS B 116 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE B  67 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL B  93 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLU B  69 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP B 143 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 205
    Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 370
      removed outlier: 3.506A  pdb=" N   GLY B 384 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418
      removed outlier: 6.318A  pdb=" N   ILE B 417 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY B 446 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU B 440 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 18
    Processing sheet with id=AA7, first strand: chain 'A' and resid 111 through 116
      removed outlier: 3.531A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ILE A  67 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   VAL A  93 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLU A  69 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TRP A 143 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A  68 " --> pdb=" O   TRP A 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.580A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370
      removed outlier: 3.619A  pdb=" N   GLY A 384 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418
      removed outlier: 4.134A  pdb=" N   GLY A 446 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLU A 440 " --> pdb=" O   PRO A 444 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19
      removed outlier: 4.806A  pdb=" N   VAL C  30 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 116
      removed outlier: 6.537A  pdb=" N   CYS C  90 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C 114 " --> pdb=" O   CYS C  90 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   PHE C  92 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   CYS C 116 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   CYS C  94 " --> pdb=" O   CYS C 116 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE C  67 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   VAL C  93 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLU C  69 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TRP C 143 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 177
      removed outlier: 3.679A  pdb=" N   PHE C 176 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU C 242 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 368
    Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 418
      removed outlier: 6.363A  pdb=" N   ILE C 417 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY C 446 " --> pdb=" O   VAL C 438 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   GLU C 440 " --> pdb=" O   PRO C 444 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18
    Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 116
      removed outlier: 3.535A  pdb=" N   VAL D 114 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ILE D  67 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   VAL D  93 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   GLU D  69 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TRP D 143 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL D  68 " --> pdb=" O   TRP D 143 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 178 through 179
      removed outlier: 3.705A  pdb=" N   ALA D 178 " --> pdb=" O   VAL D 204 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370
      removed outlier: 3.521A  pdb=" N   GLY D 384 " --> pdb=" O   VAL D 370 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 418
      removed outlier: 4.146A  pdb=" N   GLY D 446 " --> pdb=" O   VAL D 438 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   GLU D 440 " --> pdb=" O   PRO D 444 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1311 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: 2.06

  Time building geometry restraints manager: 1.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4589
        1.34 -     1.46: 2670
        1.46 -     1.58: 6429
        1.58 -     1.69: 4
        1.69 -     1.81: 104
  Bond restraints: 13796
  Sorted by residual:
  bond pdb=" CA  GLY A 297 "
       pdb=" C   GLY A 297 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 7.30e-03 1.88e+04 2.23e+01
  bond pdb=" N   ILE A 180 "
       pdb=" CA  ILE A 180 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.036 1.15e-02 7.56e+03 9.63e+00
  bond pdb=" N   ILE C  47 "
       pdb=" CA  ILE C  47 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.69e+00
  bond pdb=" N   ASP C  45 "
       pdb=" CA  ASP C  45 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.04e+00
  bond pdb=" N   THR C 182 "
       pdb=" CA  THR C 182 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.32e-02 5.74e+03 6.72e+00
  ... (remaining 13791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 18131
        1.40 -     2.80: 509
        2.80 -     4.21: 111
        4.21 -     5.61: 15
        5.61 -     7.01: 2
  Bond angle restraints: 18768
  Sorted by residual:
  angle pdb=" N   SER D 313 "
        pdb=" CA  SER D 313 "
        pdb=" C   SER D 313 "
      ideal   model   delta    sigma   weight residual
     112.54  105.53    7.01 1.22e+00 6.72e-01 3.30e+01
  angle pdb=" N   GLY C 183 "
        pdb=" CA  GLY C 183 "
        pdb=" C   GLY C 183 "
      ideal   model   delta    sigma   weight residual
     114.46  108.38    6.08 1.81e+00 3.05e-01 1.13e+01
  angle pdb=" C   LYS C  44 "
        pdb=" N   ASP C  45 "
        pdb=" CA  ASP C  45 "
      ideal   model   delta    sigma   weight residual
     120.38  116.06    4.32 1.37e+00 5.33e-01 9.94e+00
  angle pdb=" N   SER C  43 "
        pdb=" CA  SER C  43 "
        pdb=" C   SER C  43 "
      ideal   model   delta    sigma   weight residual
     113.23  109.44    3.79 1.24e+00 6.50e-01 9.34e+00
  angle pdb=" C   GLN B 367 "
        pdb=" N   MET B 368 "
        pdb=" CA  MET B 368 "
      ideal   model   delta    sigma   weight residual
     122.08  116.81    5.27 1.83e+00 2.99e-01 8.28e+00
  ... (remaining 18763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.33: 7832
       22.33 -    44.65: 324
       44.65 -    66.98: 51
       66.98 -    89.30: 11
       89.30 -   111.63: 2
  Dihedral angle restraints: 8220
    sinusoidal: 3124
      harmonic: 5096
  Sorted by residual:
  dihedral pdb=" C5A PLP D 501 "
           pdb=" O4P PLP D 501 "
           pdb=" P   PLP D 501 "
           pdb=" O1P PLP D 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43 -171.94 -111.63     1      2.00e+01 2.50e-03 3.28e+01
  dihedral pdb=" C5A PLP C 501 "
           pdb=" O4P PLP C 501 "
           pdb=" P   PLP C 501 "
           pdb=" O1P PLP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43  177.79 -101.36     1      2.00e+01 2.50e-03 2.87e+01
  dihedral pdb=" C5  PLP B 501 "
           pdb=" C5A PLP B 501 "
           pdb=" O4P PLP B 501 "
           pdb=" P   PLP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     188.31  117.64   70.66     1      2.00e+01 2.50e-03 1.61e+01
  ... (remaining 8217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1325
       0.035 -    0.070: 524
       0.070 -    0.105: 205
       0.105 -    0.140: 48
       0.140 -    0.175: 2
  Chirality restraints: 2104
  Sorted by residual:
  chirality pdb=" CA  ILE A 180 "
            pdb=" N   ILE A 180 "
            pdb=" C   ILE A 180 "
            pdb=" CB  ILE A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  ILE C  47 "
            pdb=" N   ILE C  47 "
            pdb=" C   ILE C  47 "
            pdb=" CB  ILE C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 2101 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 180 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   ILE C 180 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE C 180 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY C 181 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 294 "   -0.027 5.00e-02 4.00e+02   4.01e-02 2.57e+00
        pdb=" N   PRO B 295 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 295 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 295 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 313 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.51e+00
        pdb=" C   SER C 313 "    0.027 2.00e-02 2.50e+03
        pdb=" O   SER C 313 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C 314 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 143
        2.58 -     3.16: 12621
        3.16 -     3.74: 19431
        3.74 -     4.32: 28236
        4.32 -     4.90: 46895
  Nonbonded interactions: 107326
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 158 "
            pdb=" OE1 GLU D 195 "
     model   vdw
     2.005 3.040
  nonbonded pdb=" O   LEU D 193 "
            pdb=" OG  SER D 197 "
     model   vdw
     2.013 3.040
  nonbonded pdb=" OG1 THR D  14 "
            pdb=" O   VAL D  34 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" OH  TYR A 158 "
            pdb=" OE1 GLU A 195 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" O   LEU A 193 "
            pdb=" OG  SER A 197 "
     model   vdw
     2.096 3.040
  ... (remaining 107321 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.760
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.004   0.265  13800  Z= 0.296
  Angle     :  0.581   7.009  18768  Z= 0.319
  Chirality :  0.044   0.175   2104
  Planarity :  0.004   0.040   2472
  Dihedral  : 12.554 111.630   5012
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 32.89
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.64 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  :  3.06 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (0.18), residues: 1824
  helix: -1.69 (0.19), residues: 648
  sheet: -4.45 (0.25), residues: 200
  loop : -3.22 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  86 
 TYR   0.015   0.001   TYR D  36 
 PHE   0.007   0.001   PHE D 230 
 TRP   0.007   0.001   TRP B 310 
 HIS   0.002   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13796)
  covalent geometry    : angle       0.58097 (18768)
  hydrogen bonds       : bond        0.17269 (  454)
  hydrogen bonds       : angle       6.94894 ( 1311)
  Misc. bond           : bond        0.13428 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 281
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 GLN cc_start: 0.7381 (tt0) cc_final: 0.7157 (tt0)
REVERT: B  172 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6662 (tptt)
REVERT: B  200 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7227 (ptm160)
REVERT: B  287 ASP cc_start: 0.7236 (t0) cc_final: 0.6863 (t0)
REVERT: B  401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8210 (mtpt)
REVERT: A  260 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7485 (ttm110)
REVERT: A  363 TYR cc_start: 0.8061 (m-80) cc_final: 0.7689 (m-80)
REVERT: C   58 SER cc_start: 0.8274 (m) cc_final: 0.7955 (p)
REVERT: C   60 GLN cc_start: 0.7385 (tt0) cc_final: 0.7171 (tt0)
REVERT: C  200 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7233 (ptm160)
REVERT: C  287 ASP cc_start: 0.7246 (t0) cc_final: 0.6848 (t0)
REVERT: D  260 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7455 (ttm110)
REVERT: D  362 GLU cc_start: 0.8026 (tt0) cc_final: 0.7692 (tt0)
REVERT: D  431 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7754 (tmt-80)
REVERT: D  437 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7829 (mtm)
  outliers start: 61
  outliers final: 23
  residues processed: 325
  average time/residue: 0.1295
  time to fit residues: 59.2955
Evaluate side-chains
  214 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   44 LYS
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  437 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 ASN
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
C   5 GLN
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  20 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.131224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.107731 restraints weight = 17154.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.110304 restraints weight = 11692.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.112075 restraints weight = 9020.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.113281 restraints weight = 7565.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.113974 restraints weight = 6744.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  13800  Z= 0.210
  Angle     :  0.714   8.020  18768  Z= 0.360
  Chirality :  0.049   0.368   2104
  Planarity :  0.005   0.043   2472
  Dihedral  :  7.416  76.095   2046
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.19 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.18), residues: 1824
  helix: -1.39 (0.20), residues: 692
  sheet: -3.62 (0.28), residues: 200
  loop : -2.71 (0.19), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 260 
 TYR   0.020   0.002   TYR D  36 
 PHE   0.014   0.002   PHE C 230 
 TRP   0.014   0.001   TRP B 310 
 HIS   0.009   0.002   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (13796)
  covalent geometry    : angle       0.71438 (18768)
  hydrogen bonds       : bond        0.04536 (  454)
  hydrogen bonds       : angle       5.10720 ( 1311)
  Misc. bond           : bond        0.00042 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 SER cc_start: 0.8227 (m) cc_final: 0.7922 (p)
REVERT: B  182 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8338 (t)
REVERT: B  200 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.7199 (ptm160)
REVERT: B  401 LYS cc_start: 0.8465 (mttp) cc_final: 0.8144 (mtpt)
REVERT: A  228 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7728 (mm-30)
REVERT: A  260 ARG cc_start: 0.7932 (tpt-90) cc_final: 0.7445 (ttm110)
REVERT: A  363 TYR cc_start: 0.8056 (m-80) cc_final: 0.7717 (m-80)
REVERT: C   58 SER cc_start: 0.8198 (m) cc_final: 0.7896 (p)
REVERT: C  200 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7214 (ptm160)
REVERT: D   18 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7912 (ttt-90)
REVERT: D   35 GLU cc_start: 0.7999 (tt0) cc_final: 0.7697 (tt0)
REVERT: D  147 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8124 (pm20)
REVERT: D  228 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7679 (mm-30)
REVERT: D  362 GLU cc_start: 0.7984 (tt0) cc_final: 0.7784 (tt0)
REVERT: D  428 LYS cc_start: 0.8632 (tptm) cc_final: 0.8377 (tttt)
REVERT: D  454 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7637 (mp)
  outliers start: 33
  outliers final: 20
  residues processed: 222
  average time/residue: 0.1049
  time to fit residues: 35.2202
Evaluate side-chains
  196 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  264 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  454 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 163 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 161 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
C   6 HIS
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.134053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.110564 restraints weight = 17132.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.113134 restraints weight = 11541.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.114911 restraints weight = 8909.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.116053 restraints weight = 7456.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.116913 restraints weight = 6630.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13800  Z= 0.133
  Angle     :  0.625   6.574  18768  Z= 0.312
  Chirality :  0.046   0.293   2104
  Planarity :  0.005   0.041   2472
  Dihedral  :  6.373  63.274   2025
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.68 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.19), residues: 1824
  helix: -1.04 (0.20), residues: 696
  sheet: -2.94 (0.32), residues: 200
  loop : -2.40 (0.19), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 336 
 TYR   0.016   0.001   TYR D  36 
 PHE   0.014   0.001   PHE C 230 
 TRP   0.009   0.001   TRP B 310 
 HIS   0.007   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13796)
  covalent geometry    : angle       0.62529 (18768)
  hydrogen bonds       : bond        0.03764 (  454)
  hydrogen bonds       : angle       4.70314 ( 1311)
  Misc. bond           : bond        0.00043 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 201
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B  182 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8459 (t)
REVERT: B  200 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7073 (ptm160)
REVERT: B  401 LYS cc_start: 0.8439 (mttp) cc_final: 0.8104 (mtpt)
REVERT: B  436 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8113 (pp)
REVERT: A  228 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7720 (mm-30)
REVERT: A  260 ARG cc_start: 0.7875 (tpt-90) cc_final: 0.7339 (ttm110)
REVERT: A  363 TYR cc_start: 0.8096 (m-80) cc_final: 0.7792 (m-80)
REVERT: A  404 ASP cc_start: 0.7776 (m-30) cc_final: 0.7378 (m-30)
REVERT: A  452 ASP cc_start: 0.7556 (t0) cc_final: 0.7211 (t0)
REVERT: C  152 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7485 (mt-10)
REVERT: C  200 ARG cc_start: 0.7470 (mtp-110) cc_final: 0.7162 (ptm160)
REVERT: D   18 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8155 (ttm-80)
REVERT: D   35 GLU cc_start: 0.7974 (tt0) cc_final: 0.7636 (tt0)
REVERT: D  147 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8032 (pm20)
REVERT: D  158 TYR cc_start: 0.8278 (t80) cc_final: 0.7957 (t80)
REVERT: D  185 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7570 (m)
  outliers start: 39
  outliers final: 24
  residues processed: 228
  average time/residue: 0.1016
  time to fit residues: 34.8562
Evaluate side-chains
  205 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  264 MET
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0770
   chunk 102 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 140 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   overall best weight:    3.1544

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN
D 123 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.128157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.104561 restraints weight = 17355.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.107035 restraints weight = 11870.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.108749 restraints weight = 9234.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.109862 restraints weight = 7789.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.110712 restraints weight = 6947.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  13800  Z= 0.272
  Angle     :  0.725   7.960  18768  Z= 0.361
  Chirality :  0.049   0.150   2104
  Planarity :  0.005   0.047   2472
  Dihedral  :  6.436  60.348   2023
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.24 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.19), residues: 1824
  helix: -1.13 (0.20), residues: 704
  sheet: -2.57 (0.33), residues: 204
  loop : -2.33 (0.19), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  85 
 TYR   0.023   0.002   TYR D  36 
 PHE   0.015   0.002   PHE C 230 
 TRP   0.015   0.001   TRP B 310 
 HIS   0.010   0.002   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 (13796)
  covalent geometry    : angle       0.72456 (18768)
  hydrogen bonds       : bond        0.04840 (  454)
  hydrogen bonds       : angle       4.95691 ( 1311)
  Misc. bond           : bond        0.00099 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 162
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 ASP cc_start: 0.8569 (m-30) cc_final: 0.8356 (m-30)
REVERT: B  401 LYS cc_start: 0.8526 (mttp) cc_final: 0.8147 (mtpt)
REVERT: A   84 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8074 (pt0)
REVERT: A  185 THR cc_start: 0.8841 (m) cc_final: 0.8569 (p)
REVERT: A  228 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7870 (mm-30)
REVERT: A  260 ARG cc_start: 0.8019 (tpt-90) cc_final: 0.7479 (ttm110)
REVERT: A  363 TYR cc_start: 0.8182 (m-80) cc_final: 0.7858 (m-80)
REVERT: A  404 ASP cc_start: 0.7840 (m-30) cc_final: 0.7425 (m-30)
REVERT: D   18 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8094 (ttt90)
REVERT: D   35 GLU cc_start: 0.8017 (tt0) cc_final: 0.7751 (tt0)
REVERT: D   84 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8093 (pt0)
REVERT: D  147 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8312 (pm20)
REVERT: D  185 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (m)
REVERT: D  404 ASP cc_start: 0.7805 (m-30) cc_final: 0.7402 (m-30)
  outliers start: 56
  outliers final: 36
  residues processed: 199
  average time/residue: 0.0925
  time to fit residues: 29.1057
Evaluate side-chains
  192 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 177 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 108 optimal weight:    0.9990
   chunk 155 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A   6 HIS
A  84 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 HIS
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.134788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.111248 restraints weight = 17153.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.113927 restraints weight = 11533.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.115725 restraints weight = 8802.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.116995 restraints weight = 7365.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.117394 restraints weight = 6494.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13800  Z= 0.116
  Angle     :  0.599   6.544  18768  Z= 0.298
  Chirality :  0.044   0.136   2104
  Planarity :  0.004   0.040   2472
  Dihedral  :  5.690  49.440   2022
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.52 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.19), residues: 1824
  helix: -0.78 (0.20), residues: 700
  sheet: -2.07 (0.35), residues: 204
  loop : -2.06 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.015   0.001   TYR D  36 
 PHE   0.015   0.001   PHE C 230 
 TRP   0.006   0.001   TRP C 310 
 HIS   0.006   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13796)
  covalent geometry    : angle       0.59917 (18768)
  hydrogen bonds       : bond        0.03484 (  454)
  hydrogen bonds       : angle       4.54679 ( 1311)
  Misc. bond           : bond        0.00020 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7092 (mp0)
REVERT: B   96 ASP cc_start: 0.8540 (m-30) cc_final: 0.8323 (m-30)
REVERT: B  152 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7455 (mt-10)
REVERT: B  200 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6938 (ptm160)
REVERT: B  401 LYS cc_start: 0.8490 (mttp) cc_final: 0.8125 (mtpt)
REVERT: B  436 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8015 (pp)
REVERT: A   84 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8085 (pt0)
REVERT: A  158 TYR cc_start: 0.8204 (t80) cc_final: 0.7879 (t80)
REVERT: A  228 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7647 (mm-30)
REVERT: A  260 ARG cc_start: 0.7884 (tpt-90) cc_final: 0.7359 (ttm110)
REVERT: A  332 ASP cc_start: 0.8357 (t0) cc_final: 0.8101 (m-30)
REVERT: A  363 TYR cc_start: 0.8083 (m-80) cc_final: 0.7766 (m-80)
REVERT: A  404 ASP cc_start: 0.7876 (m-30) cc_final: 0.7513 (m-30)
REVERT: A  452 ASP cc_start: 0.7436 (t0) cc_final: 0.7131 (t0)
REVERT: C   17 VAL cc_start: 0.9390 (t) cc_final: 0.9049 (m)
REVERT: C  329 THR cc_start: 0.7440 (t) cc_final: 0.7224 (t)
REVERT: C  424 SER cc_start: 0.9012 (t) cc_final: 0.8748 (p)
REVERT: C  436 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8097 (pp)
REVERT: D   35 GLU cc_start: 0.7969 (tt0) cc_final: 0.7721 (tt0)
REVERT: D   84 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8048 (pt0)
REVERT: D  147 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8027 (pm20)
REVERT: D  158 TYR cc_start: 0.8257 (t80) cc_final: 0.7918 (t80)
REVERT: D  332 ASP cc_start: 0.8331 (t0) cc_final: 0.8102 (m-30)
REVERT: D  404 ASP cc_start: 0.7852 (m-30) cc_final: 0.7504 (m-30)
  outliers start: 42
  outliers final: 25
  residues processed: 220
  average time/residue: 0.1009
  time to fit residues: 33.5550
Evaluate side-chains
  200 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 170
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  404 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 153 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 141 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 137 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
A  84 GLN
A 123 HIS
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.132522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.108821 restraints weight = 17193.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.111406 restraints weight = 11689.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.113015 restraints weight = 8998.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.114414 restraints weight = 7586.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.115156 restraints weight = 6715.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13800  Z= 0.159
  Angle     :  0.626   6.760  18768  Z= 0.311
  Chirality :  0.046   0.171   2104
  Planarity :  0.005   0.041   2472
  Dihedral  :  5.625  64.472   2020
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.52 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.20), residues: 1824
  helix: -0.73 (0.20), residues: 700
  sheet: -1.77 (0.36), residues: 204
  loop : -1.92 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.023   0.002   TYR A 451 
 PHE   0.014   0.001   PHE C 230 
 TRP   0.009   0.001   TRP B 310 
 HIS   0.006   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (13796)
  covalent geometry    : angle       0.62560 (18768)
  hydrogen bonds       : bond        0.03861 (  454)
  hydrogen bonds       : angle       4.57894 ( 1311)
  Misc. bond           : bond        0.00041 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 165
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8008 (pt0)
REVERT: B  152 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7491 (mt-10)
REVERT: B  200 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.7034 (ptm160)
REVERT: B  401 LYS cc_start: 0.8503 (mttp) cc_final: 0.8120 (mtpt)
REVERT: B  436 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8030 (pp)
REVERT: A  158 TYR cc_start: 0.8212 (t80) cc_final: 0.7890 (t80)
REVERT: A  228 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: A  260 ARG cc_start: 0.7923 (tpt-90) cc_final: 0.7387 (ttm110)
REVERT: A  332 ASP cc_start: 0.8375 (t0) cc_final: 0.8042 (m-30)
REVERT: A  363 TYR cc_start: 0.8141 (m-80) cc_final: 0.7870 (m-80)
REVERT: A  404 ASP cc_start: 0.7908 (m-30) cc_final: 0.7525 (m-30)
REVERT: A  452 ASP cc_start: 0.7437 (t0) cc_final: 0.7166 (t0)
REVERT: C  200 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7125 (ptm160)
REVERT: C  378 MET cc_start: 0.7777 (pmm) cc_final: 0.6857 (mmm)
REVERT: C  424 SER cc_start: 0.9037 (t) cc_final: 0.8766 (p)
REVERT: C  436 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8064 (pp)
REVERT: D   35 GLU cc_start: 0.8046 (tt0) cc_final: 0.7800 (tt0)
REVERT: D  147 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8076 (pm20)
REVERT: D  332 ASP cc_start: 0.8360 (t0) cc_final: 0.8062 (m-30)
REVERT: D  404 ASP cc_start: 0.7874 (m-30) cc_final: 0.7505 (m-30)
  outliers start: 51
  outliers final: 35
  residues processed: 206
  average time/residue: 0.0979
  time to fit residues: 31.2109
Evaluate side-chains
  200 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 153 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 163 optimal weight:    3.9990
   chunk 154 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 128 optimal weight:    5.9990
   chunk 177 optimal weight:    5.9990
   chunk 131 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.131399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.107625 restraints weight = 17211.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.110227 restraints weight = 11695.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.112016 restraints weight = 9007.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.113074 restraints weight = 7584.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.113995 restraints weight = 6773.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13800  Z= 0.189
  Angle     :  0.654   7.354  18768  Z= 0.323
  Chirality :  0.047   0.155   2104
  Planarity :  0.005   0.042   2472
  Dihedral  :  5.634  63.072   2020
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.59 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.20), residues: 1824
  helix: -0.74 (0.20), residues: 700
  sheet: -1.62 (0.37), residues: 204
  loop : -1.87 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.022   0.002   TYR A 451 
 PHE   0.014   0.001   PHE C 230 
 TRP   0.010   0.001   TRP B 310 
 HIS   0.006   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (13796)
  covalent geometry    : angle       0.65390 (18768)
  hydrogen bonds       : bond        0.04086 (  454)
  hydrogen bonds       : angle       4.63422 ( 1311)
  Misc. bond           : bond        0.00057 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 160
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8701 (pt0)
REVERT: B  152 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7574 (mt-10)
REVERT: B  311 MET cc_start: 0.9131 (mmm) cc_final: 0.8919 (tpp)
REVERT: B  401 LYS cc_start: 0.8518 (mttp) cc_final: 0.8142 (mtpt)
REVERT: B  436 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8018 (pp)
REVERT: A   84 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8139 (pt0)
REVERT: A  228 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: A  332 ASP cc_start: 0.8369 (t0) cc_final: 0.8041 (m-30)
REVERT: A  363 TYR cc_start: 0.8197 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  404 ASP cc_start: 0.7878 (m-30) cc_final: 0.7498 (m-30)
REVERT: A  452 ASP cc_start: 0.7554 (t0) cc_final: 0.7209 (t0)
REVERT: C  378 MET cc_start: 0.7876 (pmm) cc_final: 0.7022 (mmm)
REVERT: C  424 SER cc_start: 0.9060 (t) cc_final: 0.8772 (p)
REVERT: C  436 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8038 (pp)
REVERT: D   35 GLU cc_start: 0.8021 (tt0) cc_final: 0.7792 (tt0)
REVERT: D  147 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8223 (pm20)
REVERT: D  332 ASP cc_start: 0.8352 (t0) cc_final: 0.8062 (m-30)
REVERT: D  404 ASP cc_start: 0.7860 (m-30) cc_final: 0.7508 (m-30)
  outliers start: 51
  outliers final: 41
  residues processed: 201
  average time/residue: 0.0955
  time to fit residues: 30.2200
Evaluate side-chains
  199 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 153
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   84 GLN
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 163 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 126 optimal weight:    0.9990
   chunk 105 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 110 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 133 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 162 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS
B  84 GLN
A  84 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.134625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.111203 restraints weight = 16938.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.113849 restraints weight = 11394.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.115611 restraints weight = 8755.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.116757 restraints weight = 7359.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.117476 restraints weight = 6544.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13800  Z= 0.124
  Angle     :  0.606   8.092  18768  Z= 0.299
  Chirality :  0.045   0.146   2104
  Planarity :  0.004   0.041   2472
  Dihedral  :  5.386  65.144   2020
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.09 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.20), residues: 1824
  helix: -0.48 (0.20), residues: 696
  sheet: -1.40 (0.37), residues: 204
  loop : -1.73 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.022   0.001   TYR A 451 
 PHE   0.011   0.001   PHE C 230 
 TRP   0.006   0.001   TRP C 310 
 HIS   0.005   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13796)
  covalent geometry    : angle       0.60580 (18768)
  hydrogen bonds       : bond        0.03423 (  454)
  hydrogen bonds       : angle       4.45659 ( 1311)
  Misc. bond           : bond        0.00027 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 168
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7318 (mp0)
REVERT: B   96 ASP cc_start: 0.8536 (m-30) cc_final: 0.8332 (m-30)
REVERT: B  152 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7486 (mt-10)
REVERT: B  200 ARG cc_start: 0.7342 (mtp-110) cc_final: 0.6892 (ptm160)
REVERT: B  401 LYS cc_start: 0.8508 (mttp) cc_final: 0.8111 (mtpt)
REVERT: B  436 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7958 (pp)
REVERT: A   84 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8164 (pt0)
REVERT: A  158 TYR cc_start: 0.8100 (t80) cc_final: 0.7778 (t80)
REVERT: A  228 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: A  332 ASP cc_start: 0.8293 (t0) cc_final: 0.8018 (m-30)
REVERT: A  363 TYR cc_start: 0.8155 (m-80) cc_final: 0.7884 (m-80)
REVERT: A  404 ASP cc_start: 0.7873 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  452 ASP cc_start: 0.7293 (t0) cc_final: 0.7029 (t0)
REVERT: C    9 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7242 (mp0)
REVERT: C  200 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7068 (ptm160)
REVERT: C  287 ASP cc_start: 0.7044 (t0) cc_final: 0.6760 (t0)
REVERT: C  378 MET cc_start: 0.7836 (pmm) cc_final: 0.7052 (mmm)
REVERT: C  424 SER cc_start: 0.9049 (t) cc_final: 0.8776 (p)
REVERT: C  436 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (pp)
REVERT: D  147 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8052 (pm20)
REVERT: D  158 TYR cc_start: 0.8271 (t80) cc_final: 0.7920 (t80)
REVERT: D  332 ASP cc_start: 0.8284 (t0) cc_final: 0.8057 (m-30)
REVERT: D  404 ASP cc_start: 0.7879 (m-30) cc_final: 0.7541 (m-30)
  outliers start: 48
  outliers final: 34
  residues processed: 205
  average time/residue: 0.0936
  time to fit residues: 30.4803
Evaluate side-chains
  203 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 142 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 137 optimal weight:    5.9990
   chunk 144 optimal weight:    0.7980
   chunk 179 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0170
   chunk 66 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   overall best weight:    2.1624

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** C  84 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 = 0.3380 r_free = 0.3380 target = 0.131237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.107602 restraints weight = 17217.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.110215 restraints weight = 11663.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.112023 restraints weight = 8959.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.113227 restraints weight = 7529.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.113521 restraints weight = 6700.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13800  Z= 0.197
  Angle     :  0.664   7.009  18768  Z= 0.327
  Chirality :  0.047   0.153   2104
  Planarity :  0.005   0.042   2472
  Dihedral  :  5.405  61.677   2018
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.37 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.20), residues: 1824
  helix: -0.57 (0.20), residues: 696
  sheet: -1.14 (0.37), residues: 208
  loop : -1.74 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 260 
 TYR   0.023   0.002   TYR A 451 
 PHE   0.013   0.001   PHE A 306 
 TRP   0.010   0.001   TRP B 310 
 HIS   0.007   0.001   HIS D 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (13796)
  covalent geometry    : angle       0.66366 (18768)
  hydrogen bonds       : bond        0.04140 (  454)
  hydrogen bonds       : angle       4.61813 ( 1311)
  Misc. bond           : bond        0.00061 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 164
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7273 (mp0)
REVERT: B  152 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7590 (mt-10)
REVERT: B  287 ASP cc_start: 0.7276 (t0) cc_final: 0.6994 (t0)
REVERT: B  401 LYS cc_start: 0.8534 (mttp) cc_final: 0.8139 (mtpt)
REVERT: B  430 LEU cc_start: 0.8559 (mp) cc_final: 0.8357 (mp)
REVERT: B  436 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8052 (pp)
REVERT: A   84 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8321 (pt0)
REVERT: A  228 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7644 (mm-30)
REVERT: A  332 ASP cc_start: 0.8327 (t0) cc_final: 0.8012 (m-30)
REVERT: A  363 TYR cc_start: 0.8227 (m-80) cc_final: 0.7978 (m-80)
REVERT: A  404 ASP cc_start: 0.7858 (m-30) cc_final: 0.7485 (m-30)
REVERT: A  452 ASP cc_start: 0.7356 (t0) cc_final: 0.7010 (t0)
REVERT: C  287 ASP cc_start: 0.7093 (t0) cc_final: 0.6861 (t0)
REVERT: C  378 MET cc_start: 0.7880 (pmm) cc_final: 0.7216 (mmm)
REVERT: C  424 SER cc_start: 0.9074 (t) cc_final: 0.8788 (p)
REVERT: C  436 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8059 (pp)
REVERT: D  147 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8196 (pm20)
REVERT: D  332 ASP cc_start: 0.8308 (t0) cc_final: 0.8034 (m-30)
REVERT: D  404 ASP cc_start: 0.7855 (m-30) cc_final: 0.7503 (m-30)
  outliers start: 47
  outliers final: 39
  residues processed: 201
  average time/residue: 0.0848
  time to fit residues: 27.3865
Evaluate side-chains
  201 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 158
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0020
   chunk 118 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 131 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.135473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.112035 restraints weight = 16947.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.114693 restraints weight = 11405.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.116486 restraints weight = 8738.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117640 restraints weight = 7317.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.118284 restraints weight = 6493.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13800  Z= 0.113
  Angle     :  0.605   8.211  18768  Z= 0.297
  Chirality :  0.045   0.137   2104
  Planarity :  0.004   0.042   2472
  Dihedral  :  5.228  64.687   2018
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.80 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.20), residues: 1824
  helix: -0.33 (0.20), residues: 692
  sheet: -0.91 (0.37), residues: 212
  loop : -1.58 (0.21), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.022   0.001   TYR A 451 
 PHE   0.011   0.001   PHE C 230 
 TRP   0.005   0.001   TRP C 310 
 HIS   0.004   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13796)
  covalent geometry    : angle       0.60484 (18768)
  hydrogen bonds       : bond        0.03295 (  454)
  hydrogen bonds       : angle       4.42972 ( 1311)
  Misc. bond           : bond        0.00028 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 172
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7238 (mp0)
REVERT: B  200 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.6801 (ptm160)
REVERT: B  260 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8273 (tpp80)
REVERT: B  311 MET cc_start: 0.9139 (tpp) cc_final: 0.8364 (tpp)
REVERT: B  401 LYS cc_start: 0.8503 (mttp) cc_final: 0.8120 (mtpt)
REVERT: B  436 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8047 (pp)
REVERT: A   84 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8353 (pt0)
REVERT: A  158 TYR cc_start: 0.8115 (t80) cc_final: 0.7785 (t80)
REVERT: A  228 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7459 (mm-30)
REVERT: A  332 ASP cc_start: 0.8310 (t0) cc_final: 0.8004 (m-30)
REVERT: A  363 TYR cc_start: 0.8169 (m-80) cc_final: 0.7929 (m-80)
REVERT: A  404 ASP cc_start: 0.7826 (m-30) cc_final: 0.7482 (m-30)
REVERT: A  452 ASP cc_start: 0.7105 (t0) cc_final: 0.6852 (t0)
REVERT: C  200 ARG cc_start: 0.7428 (mtp-110) cc_final: 0.7048 (ptm160)
REVERT: C  378 MET cc_start: 0.7809 (pmm) cc_final: 0.7064 (mmm)
REVERT: C  424 SER cc_start: 0.9068 (t) cc_final: 0.8809 (p)
REVERT: C  436 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8039 (pp)
REVERT: D  147 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8037 (pm20)
REVERT: D  158 TYR cc_start: 0.8190 (t80) cc_final: 0.7868 (t80)
REVERT: D  228 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7411 (mm-30)
REVERT: D  260 ARG cc_start: 0.8532 (tpp80) cc_final: 0.7892 (ttm110)
REVERT: D  296 ASP cc_start: 0.8369 (t0) cc_final: 0.7851 (m-30)
REVERT: D  332 ASP cc_start: 0.8225 (t0) cc_final: 0.8017 (m-30)
REVERT: D  404 ASP cc_start: 0.7818 (m-30) cc_final: 0.7498 (m-30)
  outliers start: 42
  outliers final: 34
  residues processed: 204
  average time/residue: 0.0978
  time to fit residues: 30.8362
Evaluate side-chains
  203 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 149 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 153 optimal weight:    0.0980
   chunk 166 optimal weight:    3.9990
   chunk 178 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 155 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 151 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 139 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.136302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.112841 restraints weight = 16998.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.115558 restraints weight = 11369.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.117436 restraints weight = 8674.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.118659 restraints weight = 7232.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.119378 restraints weight = 6394.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13800  Z= 0.117
  Angle     :  0.599   7.879  18768  Z= 0.294
  Chirality :  0.045   0.136   2104
  Planarity :  0.004   0.042   2472
  Dihedral  :  5.115  64.470   2017
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.09 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.20), residues: 1824
  helix: -0.22 (0.20), residues: 692
  sheet: -0.69 (0.37), residues: 212
  loop : -1.48 (0.21), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 260 
 TYR   0.021   0.001   TYR A 451 
 PHE   0.010   0.001   PHE C 230 
 TRP   0.006   0.001   TRP A 310 
 HIS   0.004   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13796)
  covalent geometry    : angle       0.59884 (18768)
  hydrogen bonds       : bond        0.03344 (  454)
  hydrogen bonds       : angle       4.38643 ( 1311)
  Misc. bond           : bond        0.00026 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1894.39 seconds
wall clock time: 33 minutes 31.23 seconds (2011.23 seconds total)