Starting phenix.real_space_refine
on Thu Feb  5 13:04:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kuc_62576/02_2026/9kuc_62576.map"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.051
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C   10981      2.51       5
     N    2922      2.21       5
     O    3263      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17214
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2909
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 18, 'TRANS': 358}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2833
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 18, 'TRANS': 349}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2833
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 18, 'TRANS': 349}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2927
          Classifications: {'peptide': 379}
          Link IDs: {'PTRANS': 18, 'TRANS': 360}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2909
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 18, 'TRANS': 358}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2803
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 18, 'TRANS': 345}
          Chain breaks: 2
  Residues with excluded nonbonded symmetry interactions: 12
    residue:
      pdb=" N   GLY A 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 261 " occ=0.00
    residue:
      pdb=" N   GLY A 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 281 " occ=0.00
    residue:
      pdb=" N   GLY B 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY B 261 " occ=0.00
    residue:
      pdb=" N   GLY B 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY B 281 " occ=0.00
    residue:
      pdb=" N   GLY C 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY C 261 " occ=0.00
    residue:
      pdb=" N   GLY C 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY C 281 " occ=0.00
    residue:
      pdb=" N   GLY D 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY D 261 " occ=0.00
    residue:
      pdb=" N   GLY D 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY D 281 " occ=0.00
    residue:
      pdb=" N   GLY E 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY E 261 " occ=0.00
    residue:
      pdb=" N   GLY E 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY E 281 " occ=0.00
    residue:
      pdb=" N   GLY F 261 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY F 261 " occ=0.00
    residue:
      pdb=" N   GLY F 281 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY F 281 " occ=0.00
  Time building chain proxies: 4.01, per 1000 atoms: 0.23
  Number of scatterers: 17214
  At special positions: 0
  Unit cell: (154.38, 156.87, 94.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    3263      8.00
     N    2922      7.00
     C   10981      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 716.0 milliseconds
  

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4108

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 34 sheets defined
      35.2% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 60
      removed outlier: 3.657A  pdb=" N   GLU A  56 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 83
      removed outlier: 3.589A  pdb=" N   SER A  80 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ASP A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.890A  pdb=" N   LYS A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A  99 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 134
      removed outlier: 3.539A  pdb=" N   GLY A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 162
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.688A  pdb=" N   ALA A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 312
    Processing helix  chain 'A' and resid 419 through 426
    Processing helix  chain 'A' and resid 426 through 447
      removed outlier: 3.658A  pdb=" N   LYS A 430 " --> pdb=" O   ASP A 426 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   TRP A 439 " --> pdb=" O   SER A 435 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP A 447 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 60
      removed outlier: 4.270A  pdb=" N   VAL B  53 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU B  56 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 81
      removed outlier: 3.931A  pdb=" N   THR B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 99
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 128 through 134
    Processing helix  chain 'B' and resid 153 through 162
    Processing helix  chain 'B' and resid 217 through 229
    Processing helix  chain 'B' and resid 246 through 258
      removed outlier: 3.837A  pdb=" N   PHE B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 312
      removed outlier: 3.693A  pdb=" N   VAL B 305 " --> pdb=" O   ALA B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 4.043A  pdb=" N   ARG B 353 " --> pdb=" O   PRO B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 426
    Processing helix  chain 'B' and resid 426 through 446
    Processing helix  chain 'C' and resid 46 through 61
      removed outlier: 3.666A  pdb=" N   PHE C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 73
    Processing helix  chain 'C' and resid 74 through 83
      removed outlier: 3.657A  pdb=" N   SER C  80 " --> pdb=" O   GLU C  76 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN C  81 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 100
    Processing helix  chain 'C' and resid 128 through 133
    Processing helix  chain 'C' and resid 153 through 162
    Processing helix  chain 'C' and resid 217 through 229
    Processing helix  chain 'C' and resid 246 through 258
      removed outlier: 4.080A  pdb=" N   LEU C 256 " --> pdb=" O   GLY C 252 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   PHE C 257 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 312
      removed outlier: 3.512A  pdb=" N   ALA C 306 " --> pdb=" O   SER C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 419 through 425
    Processing helix  chain 'C' and resid 426 through 447
      removed outlier: 3.542A  pdb=" N   ALA C 432 " --> pdb=" O   GLN C 428 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TRP C 439 " --> pdb=" O   SER C 435 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   MET C 446 " --> pdb=" O   VAL C 442 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ASP C 447 " --> pdb=" O   ASP C 443 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 60
      removed outlier: 3.540A  pdb=" N   VAL D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU D  56 " --> pdb=" O   ASN D  52 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU D  58 " --> pdb=" O   VAL D  54 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LYS D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 83
      removed outlier: 3.549A  pdb=" N   MET D  71 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR D  72 " --> pdb=" O   SER D  68 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU D  76 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASP D  83 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 100
      removed outlier: 4.019A  pdb=" N   LYS D  95 " --> pdb=" O   GLU D  91 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU D  96 " --> pdb=" O   LYS D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 133
    Processing helix  chain 'D' and resid 148 through 152
    Processing helix  chain 'D' and resid 153 through 162
      removed outlier: 3.969A  pdb=" N   ASN D 159 " --> pdb=" O   ASP D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 217 through 229
    Processing helix  chain 'D' and resid 246 through 256
      removed outlier: 3.646A  pdb=" N   ALA D 250 " --> pdb=" O   LEU D 246 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY D 252 " --> pdb=" O   ASN D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 274
    Processing helix  chain 'D' and resid 301 through 312
      removed outlier: 3.546A  pdb=" N   GLY D 307 " --> pdb=" O   GLU D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 413 through 415
      No H-bonds generated for 'chain 'D' and resid 413 through 415'
    Processing helix  chain 'D' and resid 419 through 424
    Processing helix  chain 'D' and resid 426 through 445
    Processing helix  chain 'E' and resid 47 through 60
      removed outlier: 4.050A  pdb=" N   SER E  51 " --> pdb=" O   PHE E  47 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS E  59 " --> pdb=" O   SER E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 83
      removed outlier: 3.526A  pdb=" N   ILE E  70 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 99
      removed outlier: 4.292A  pdb=" N   ALA E  99 " --> pdb=" O   LYS E  95 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 107
      removed outlier: 4.025A  pdb=" N   GLY E 107 " --> pdb=" O   GLU E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 133
    Processing helix  chain 'E' and resid 153 through 162
    Processing helix  chain 'E' and resid 217 through 228
    Processing helix  chain 'E' and resid 246 through 257
      removed outlier: 4.335A  pdb=" N   GLY E 252 " --> pdb=" O   ASN E 248 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE E 257 " --> pdb=" O   LEU E 253 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 270 through 274
    Processing helix  chain 'E' and resid 300 through 312
      removed outlier: 3.829A  pdb=" N   ALA E 306 " --> pdb=" O   SER E 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 419 through 425
    Processing helix  chain 'E' and resid 427 through 446
      removed outlier: 3.657A  pdb=" N   TRP E 439 " --> pdb=" O   SER E 435 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   MET E 446 " --> pdb=" O   VAL E 442 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 447 through 447
      No H-bonds generated for 'chain 'E' and resid 447 through 447'
    Processing helix  chain 'F' and resid 45 through 46
      No H-bonds generated for 'chain 'F' and resid 45 through 46'
    Processing helix  chain 'F' and resid 47 through 60
      removed outlier: 3.525A  pdb=" N   SER F  55 " --> pdb=" O   SER F  51 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU F  56 " --> pdb=" O   ASN F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 83
      removed outlier: 3.711A  pdb=" N   MET F  71 " --> pdb=" O   ILE F  67 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU F  76 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY F  77 " --> pdb=" O   LYS F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 99
    Processing helix  chain 'F' and resid 114 through 118
    Processing helix  chain 'F' and resid 128 through 134
      removed outlier: 3.780A  pdb=" N   LYS F 132 " --> pdb=" O   THR F 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 154 through 160
    Processing helix  chain 'F' and resid 217 through 228
    Processing helix  chain 'F' and resid 246 through 256
    Processing helix  chain 'F' and resid 300 through 312
      removed outlier: 3.822A  pdb=" N   ALA F 306 " --> pdb=" O   SER F 302 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 419 through 426
      removed outlier: 3.548A  pdb=" N   ILE F 423 " --> pdb=" O   THR F 419 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP F 426 " --> pdb=" O   MET F 422 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 426 through 447
      removed outlier: 3.695A  pdb=" N   LYS F 430 " --> pdb=" O   ASP F 426 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TRP F 439 " --> pdb=" O   SER F 435 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89
      removed outlier: 7.177A  pdb=" N   TYR A 277 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   SER A 265 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU A 275 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.728A  pdb=" N   ALA A 339 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   VAL A 334 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   LYS A 341 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   THR A 343 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   MET A 330 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 345 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 112
      removed outlier: 7.647A  pdb=" N   THR A 111 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148
      removed outlier: 4.675A  pdb=" N   LYS A 143 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 200
      removed outlier: 3.537A  pdb=" N   LYS A 199 " --> pdb=" O   TYR A 208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 89
      removed outlier: 3.560A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG B 346 " --> pdb=" O   LYS B 267 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS B 267 " --> pdb=" O   ARG B 346 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   VAL B 262 " --> pdb=" O   ALA B 279 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA B 279 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89
      removed outlier: 3.560A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLU B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   THR B 344 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   VAL B 328 " --> pdb=" O   THR B 344 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 173
    Processing sheet with id=AB1, first strand: chain 'B' and resid 292 through 294
      removed outlier: 6.326A  pdb=" N   VAL B 292 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 364 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 88
      removed outlier: 3.795A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 277 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88
      removed outlier: 4.311A  pdb=" N   ILE C 340 " --> pdb=" O   LEU C 332 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ILE C 342 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   MET C 330 " --> pdb=" O   ILE C 342 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   VAL C 328 " --> pdb=" O   THR C 344 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 115
    Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148
      removed outlier: 5.837A  pdb=" N   ILE C 141 " --> pdb=" O   VAL C 174 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   VAL C 174 " --> pdb=" O   ILE C 141 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS C 143 " --> pdb=" O   THR C 172 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE C 169 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 196 through 197
      removed outlier: 3.658A  pdb=" N   TYR C 197 " --> pdb=" O   ARG C 210 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   LEU C 207 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ASP C 238 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL C 209 " --> pdb=" O   ASP C 238 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 201
      removed outlier: 6.837A  pdb=" N   LYS C 200 " --> pdb=" O   VAL C 418 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'C' and resid 293 through 294
    Processing sheet with id=AB9, first strand: chain 'D' and resid 87 through 88
      removed outlier: 4.184A  pdb=" N   LEU D 332 " --> pdb=" O   ILE D 340 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL D 328 " --> pdb=" O   THR D 344 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 110 through 112
      removed outlier: 6.758A  pdb=" N   THR D 111 " --> pdb=" O   ILE D 122 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 175
      removed outlier: 3.887A  pdb=" N   ILE D 169 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE D 186 " --> pdb=" O   ILE D 169 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   ARG D 175 " --> pdb=" O   LYS D 180 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   LYS D 180 " --> pdb=" O   ARG D 175 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 196 through 198
      removed outlier: 3.604A  pdb=" N   TYR D 197 " --> pdb=" O   ARG D 210 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 200 through 201
      removed outlier: 7.254A  pdb=" N   LYS D 200 " --> pdb=" O   VAL D 418 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'D' and resid 293 through 294
    Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 89
    Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 89
      removed outlier: 5.480A  pdb=" N   LYS E 341 " --> pdb=" O   LEU E 332 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   LEU E 332 " --> pdb=" O   LYS E 341 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   THR E 343 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   MET E 330 " --> pdb=" O   THR E 343 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA E 345 " --> pdb=" O   VAL E 328 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 111 through 114
      removed outlier: 7.373A  pdb=" N   THR E 111 " --> pdb=" O   ILE E 122 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'E' and resid 147 through 148
      removed outlier: 5.457A  pdb=" N   ILE E 141 " --> pdb=" O   VAL E 174 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL E 174 " --> pdb=" O   ILE E 141 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS E 143 " --> pdb=" O   THR E 172 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 197 through 201
      removed outlier: 3.687A  pdb=" N   TYR E 197 " --> pdb=" O   ARG E 210 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG E 210 " --> pdb=" O   TYR E 197 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   TYR E 206 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   VAL E 236 " --> pdb=" O   PRO E 205 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LEU E 207 " --> pdb=" O   VAL E 236 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   ASP E 238 " --> pdb=" O   LEU E 207 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   VAL E 209 " --> pdb=" O   ASP E 238 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 292 through 294
      removed outlier: 6.250A  pdb=" N   VAL E 292 " --> pdb=" O   ILE E 318 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 87 through 89
      removed outlier: 6.694A  pdb=" N   GLU F 338 " --> pdb=" O   VAL F 334 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE F 342 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET F 330 " --> pdb=" O   ILE F 342 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL F 328 " --> pdb=" O   THR F 344 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'F' and resid 140 through 141
      removed outlier: 3.633A  pdb=" N   ASN F 140 " --> pdb=" O   VAL F 174 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL F 174 " --> pdb=" O   ASN F 140 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ILE F 173 " --> pdb=" O   LYS F 180 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LYS F 180 " --> pdb=" O   ILE F 173 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'F' and resid 197 through 200
      removed outlier: 5.695A  pdb=" N   TYR F 208 " --> pdb=" O   LYS F 199 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'F' and resid 262 through 265
      removed outlier: 7.207A  pdb=" N   TYR F 277 " --> pdb=" O   LEU F 263 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'F' and resid 291 through 293
      removed outlier: 6.113A  pdb=" N   VAL F 292 " --> pdb=" O   ILE F 318 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   ILE F 317 " --> pdb=" O   ILE F 364 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD7

    583 hydrogen bonds defined for protein.
    1632 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: 2.51

  Time building geometry restraints manager: 1.71 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: 5582
        1.34 -     1.46: 3182
        1.46 -     1.58: 8611
        1.58 -     1.70: 0
        1.70 -     1.81: 96
  Bond restraints: 17471
  Sorted by residual:
  bond pdb=" N   MET F 446 "
       pdb=" CA  MET F 446 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.35e-02 5.49e+03 5.66e+00
  bond pdb=" N   GLU F 444 "
       pdb=" CA  GLU F 444 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.20e-02 6.94e+03 5.57e+00
  bond pdb=" N   LYS F 445 "
       pdb=" CA  LYS F 445 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.27e-02 6.20e+03 4.38e+00
  bond pdb=" N   HIS F  45 "
       pdb=" CA  HIS F  45 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  bond pdb=" N   HIS B  45 "
       pdb=" CA  HIS B  45 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  ... (remaining 17466 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 23454
        3.14 -     6.28: 87
        6.28 -     9.42: 1
        9.42 -    12.56: 0
       12.56 -    15.70: 1
  Bond angle restraints: 23543
  Sorted by residual:
  angle pdb=" CG1 ILE F 169 "
        pdb=" CB  ILE F 169 "
        pdb=" CG2 ILE F 169 "
      ideal   model   delta    sigma   weight residual
     110.70  126.40  -15.70 3.00e+00 1.11e-01 2.74e+01
  angle pdb=" N   ILE D 304 "
        pdb=" CA  ILE D 304 "
        pdb=" C   ILE D 304 "
      ideal   model   delta    sigma   weight residual
     113.42  109.39    4.03 1.17e+00 7.31e-01 1.19e+01
  angle pdb=" N   ASP F 443 "
        pdb=" CA  ASP F 443 "
        pdb=" C   ASP F 443 "
      ideal   model   delta    sigma   weight residual
     111.28  107.65    3.63 1.09e+00 8.42e-01 1.11e+01
  angle pdb=" CA  GLY E 369 "
        pdb=" C   GLY E 369 "
        pdb=" N   LYS E 370 "
      ideal   model   delta    sigma   weight residual
     114.58  117.28   -2.70 8.60e-01 1.35e+00 9.89e+00
  angle pdb=" CA  ILE F 169 "
        pdb=" CB  ILE F 169 "
        pdb=" CG2 ILE F 169 "
      ideal   model   delta    sigma   weight residual
     110.50  115.66   -5.16 1.70e+00 3.46e-01 9.20e+00
  ... (remaining 23538 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 9782
       17.91 -    35.82: 833
       35.82 -    53.73: 174
       53.73 -    71.64: 34
       71.64 -    89.55: 24
  Dihedral angle restraints: 10847
    sinusoidal: 4453
      harmonic: 6394
  Sorted by residual:
  dihedral pdb=" CA  PRO B 205 "
           pdb=" C   PRO B 205 "
           pdb=" N   TYR B 206 "
           pdb=" CA  TYR B 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.50  -36.50     0      5.00e+00 4.00e-02 5.33e+01
  dihedral pdb=" CA  GLY E 261 "
           pdb=" C   GLY E 261 "
           pdb=" N   VAL E 262 "
           pdb=" CA  VAL E 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.43   23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  TYR E  61 "
           pdb=" C   TYR E  61 "
           pdb=" N   VAL E  62 "
           pdb=" CA  VAL E  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 10844 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.353: 2741
       0.353 -    0.707: 2
       0.707 -    1.060: 0
       1.060 -    1.414: 0
       1.414 -    1.767: 1
  Chirality restraints: 2744
  Sorted by residual:
  chirality pdb=" CB  ILE F 169 "
            pdb=" CA  ILE F 169 "
            pdb=" CG1 ILE F 169 "
            pdb=" CG2 ILE F 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    0.88    1.77 2.00e-01 2.50e+01 7.81e+01
  chirality pdb=" CA  GLU F 375 "
            pdb=" N   GLU F 375 "
            pdb=" C   GLU F 375 "
            pdb=" CB  GLU F 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.42e+00
  chirality pdb=" CA  ARG B 115 "
            pdb=" N   ARG B 115 "
            pdb=" C   ARG B 115 "
            pdb=" CB  ARG B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.14e+00
  ... (remaining 2741 not shown)

  Planarity restraints: 2993
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 180 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO E 181 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 181 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 181 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 164 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.54e+00
        pdb=" N   PRO E 165 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO E 165 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 165 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 164 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO C 165 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 165 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 165 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2990 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 7020
        2.90 -     3.40: 18001
        3.40 -     3.90: 26727
        3.90 -     4.40: 30824
        4.40 -     4.90: 51087
  Nonbonded interactions: 133659
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 145 "
            pdb=" OE1 GLU A 147 "
     model   vdw
     2.400 3.040
  nonbonded pdb=" OE2 GLU D 303 "
            pdb=" OG1 THR D 322 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" O   VAL D 264 "
            pdb=" O   LEU D 275 "
     model   vdw
     2.443 3.040
  nonbonded pdb=" OD1 ASP E 155 "
            pdb=" N   ASP E 156 "
     model   vdw
     2.446 3.120
  nonbonded pdb=" OG  SER C 300 "
            pdb=" N   ALA C 301 "
     model   vdw
     2.452 3.120
  ... (remaining 133654 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 45 through 99 or resid 105 through 379 or resid 415 throug \ 
h 447))
  selection = (chain 'B' and (resid 45 through 99 or resid 105 through 447))
  selection = (chain 'C' and (resid 45 through 99 or resid 105 through 447))
  selection = (chain 'D' and (resid 45 through 99 or resid 105 through 379 or resid 413 or res \ 
id 416 through 447))
  selection = (chain 'E' and (resid 45 through 99 or resid 105 through 379 or resid 415 throug \ 
h 447))
  selection = (chain 'F' and (resid 45 through 379 or resid 415 through 447))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.180
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     14.690
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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      :  0.002   0.033  17471  Z= 0.117
  Angle     :  0.534  15.698  23543  Z= 0.285
  Chirality :  0.056   1.767   2744
  Planarity :  0.004   0.043   2993
  Dihedral  : 14.651  89.547   6739
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 13.54 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.35 (0.18), residues: 2207
  helix:  0.30 (0.21), residues: 696
  sheet: -2.35 (0.29), residues: 296
  loop : -1.20 (0.18), residues: 1215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 314 
 TYR   0.011   0.001   TYR B 197 
 PHE   0.008   0.001   PHE F 323 
 TRP   0.007   0.001   TRP B 439 
 HIS   0.003   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (17471)
  covalent geometry    : angle       0.53441 (23543)
  hydrogen bonds       : bond        0.23298 (  570)
  hydrogen bonds       : angle       8.76963 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
REVERT: B  323 PHE cc_start: 0.8303 (t80) cc_final: 0.7906 (t80)
REVERT: C   47 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6553 (t80)
REVERT: C  300 SER cc_start: 0.8750 (t) cc_final: 0.8466 (p)
REVERT: D  114 MET cc_start: 0.1910 (mmt) cc_final: 0.1155 (tpp)
REVERT: D  162 ARG cc_start: 0.7045 (mmm-85) cc_final: 0.6540 (mpt180)
REVERT: E   61 TYR cc_start: 0.5941 (m-80) cc_final: 0.4954 (m-80)
REVERT: E  105 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6635 (m-80)
REVERT: E  152 MET cc_start: 0.7197 (ttp) cc_final: 0.6934 (ttp)
REVERT: F   71 MET cc_start: 0.8413 (mmt) cc_final: 0.8170 (mmt)
  outliers start: 14
  outliers final: 8
  residues processed: 148
  average time/residue: 0.1209
  time to fit residues: 27.0537
Evaluate side-chains
  122 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 216 optimal weight:    7.9990
   chunk 98 optimal weight:    0.5980
   chunk 194 optimal weight:   40.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    6.9990
   chunk 212 optimal weight:    9.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 312 HIS
B 329 GLN
B 356 GLN
F 312 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.150861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.107487 restraints weight = 35469.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.108375 restraints weight = 23822.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.108154 restraints weight = 18533.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.109173 restraints weight = 19399.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.109104 restraints weight = 16927.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17471  Z= 0.129
  Angle     :  0.579   8.929  23543  Z= 0.300
  Chirality :  0.046   0.268   2744
  Planarity :  0.004   0.041   2993
  Dihedral  :  5.136  52.476   2368
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.90 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.11 (0.18), residues: 2207
  helix:  0.60 (0.20), residues: 716
  sheet: -2.40 (0.29), residues: 292
  loop : -1.10 (0.18), residues: 1199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 282 
 TYR   0.011   0.001   TYR E 208 
 PHE   0.011   0.001   PHE F  94 
 TRP   0.006   0.001   TRP C 439 
 HIS   0.003   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (17471)
  covalent geometry    : angle       0.57928 (23543)
  hydrogen bonds       : bond        0.04385 (  570)
  hydrogen bonds       : angle       5.57971 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  285 TYR cc_start: 0.8290 (m-80) cc_final: 0.7904 (m-10)
REVERT: B  256 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8722 (tp)
REVERT: B  330 MET cc_start: 0.7993 (pmm) cc_final: 0.7782 (pmm)
REVERT: C   47 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6397 (t80)
REVERT: D   58 GLU cc_start: 0.7289 (tp30) cc_final: 0.6985 (tp30)
REVERT: D  114 MET cc_start: 0.2014 (mmt) cc_final: 0.1425 (tpp)
REVERT: D  131 TYR cc_start: 0.6525 (t80) cc_final: 0.6167 (t80)
REVERT: D  251 VAL cc_start: 0.7725 (t) cc_final: 0.7509 (p)
REVERT: E   61 TYR cc_start: 0.5949 (m-80) cc_final: 0.5066 (m-80)
REVERT: E  152 MET cc_start: 0.7394 (ttp) cc_final: 0.7003 (tmm)
REVERT: E  164 LYS cc_start: 0.8333 (tptt) cc_final: 0.8051 (tptt)
REVERT: F  114 MET cc_start: -0.0375 (ttt) cc_final: -0.1625 (mtm)
  outliers start: 40
  outliers final: 16
  residues processed: 166
  average time/residue: 0.1180
  time to fit residues: 30.4662
Evaluate side-chains
  132 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 144 optimal weight:    0.4980
   chunk 160 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0070
   chunk 173 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
B 329 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.151499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.108279 restraints weight = 35729.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.108537 restraints weight = 23472.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.109569 restraints weight = 19607.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.109853 restraints weight = 19125.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.110074 restraints weight = 18362.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17471  Z= 0.117
  Angle     :  0.556   9.910  23543  Z= 0.283
  Chirality :  0.046   0.198   2744
  Planarity :  0.004   0.047   2993
  Dihedral  :  4.800  50.334   2361
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.17 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.18), residues: 2207
  helix:  0.81 (0.20), residues: 717
  sheet: -2.11 (0.30), residues: 278
  loop : -1.11 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 346 
 TYR   0.009   0.001   TYR F 197 
 PHE   0.011   0.001   PHE B 323 
 TRP   0.006   0.001   TRP C 439 
 HIS   0.005   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (17471)
  covalent geometry    : angle       0.55557 (23543)
  hydrogen bonds       : bond        0.03776 (  570)
  hydrogen bonds       : angle       4.97022 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 137
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6710 (mtt) cc_final: 0.6439 (mtt)
REVERT: A  285 TYR cc_start: 0.8229 (m-80) cc_final: 0.7907 (m-10)
REVERT: B  256 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8766 (tp)
REVERT: B  330 MET cc_start: 0.8138 (pmm) cc_final: 0.7850 (pmm)
REVERT: C   47 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6396 (t80)
REVERT: C  152 MET cc_start: 0.7015 (mtt) cc_final: 0.6812 (mtt)
REVERT: D   58 GLU cc_start: 0.7229 (tp30) cc_final: 0.6980 (tp30)
REVERT: D  114 MET cc_start: 0.1866 (mmt) cc_final: 0.1312 (tpp)
REVERT: D  131 TYR cc_start: 0.6433 (t80) cc_final: 0.6096 (t80)
REVERT: E   61 TYR cc_start: 0.5882 (m-80) cc_final: 0.5086 (m-80)
REVERT: E  152 MET cc_start: 0.7459 (ttp) cc_final: 0.7171 (tmm)
REVERT: E  164 LYS cc_start: 0.8365 (tptt) cc_final: 0.8116 (tptt)
REVERT: F  114 MET cc_start: -0.0688 (ttt) cc_final: -0.1822 (mtm)
REVERT: F  152 MET cc_start: 0.3848 (tpt) cc_final: 0.2569 (tmm)
  outliers start: 54
  outliers final: 25
  residues processed: 184
  average time/residue: 0.1158
  time to fit residues: 33.6626
Evaluate side-chains
  148 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  178 GLU
Chi-restraints excluded: chain C residue  322 THR
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  196 VAL
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 125 optimal weight:    6.9990
   chunk 188 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 147 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 143 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0870
   chunk 205 optimal weight:    6.9990
   chunk 192 optimal weight:    9.9990
   overall best weight:    2.7764

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
C 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.148492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107175 restraints weight = 35547.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.106524 restraints weight = 23900.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106288 restraints weight = 21493.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.106792 restraints weight = 21002.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.106783 restraints weight = 19986.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  17471  Z= 0.209
  Angle     :  0.617   8.366  23543  Z= 0.315
  Chirality :  0.048   0.177   2744
  Planarity :  0.004   0.050   2993
  Dihedral  :  5.133  58.204   2358
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.57 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 14.06 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.08 (0.18), residues: 2207
  helix:  0.69 (0.20), residues: 710
  sheet: -2.23 (0.30), residues: 275
  loop : -1.20 (0.18), residues: 1222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 346 
 TYR   0.016   0.002   TYR E 197 
 PHE   0.026   0.002   PHE A 105 
 TRP   0.008   0.001   TRP D 439 
 HIS   0.006   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (17471)
  covalent geometry    : angle       0.61657 (23543)
  hydrogen bonds       : bond        0.04367 (  570)
  hydrogen bonds       : angle       5.08719 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 121
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6806 (mtt) cc_final: 0.6301 (mtt)
REVERT: B  256 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8728 (tp)
REVERT: C  178 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6847 (tm-30)
REVERT: D  114 MET cc_start: 0.1703 (mmt) cc_final: 0.1077 (tpp)
REVERT: D  131 TYR cc_start: 0.6138 (t80) cc_final: 0.5778 (t80)
REVERT: D  162 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.6636 (mpt180)
REVERT: E  164 LYS cc_start: 0.8482 (tptt) cc_final: 0.8255 (tptt)
  outliers start: 77
  outliers final: 46
  residues processed: 188
  average time/residue: 0.1144
  time to fit residues: 34.1772
Evaluate side-chains
  157 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  178 GLU
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  342 ILE
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  182 LEU
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 170 optimal weight:    0.8980
   chunk 131 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 147 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 168 optimal weight:    6.9990
   chunk 179 optimal weight:    9.9990
   chunk 114 optimal weight:    0.0770
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.1944

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

Flipped N/Q/H residues before XYZ refinement:
C 329 GLN
D  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.149292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.107973 restraints weight = 35379.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.107016 restraints weight = 23157.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.106628 restraints weight = 22708.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107375 restraints weight = 21685.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.107585 restraints weight = 19226.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  17471  Z= 0.172
  Angle     :  0.587   8.823  23543  Z= 0.299
  Chirality :  0.047   0.209   2744
  Planarity :  0.004   0.045   2993
  Dihedral  :  4.963  47.400   2356
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.66 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.84 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.09 (0.18), residues: 2207
  helix:  0.71 (0.20), residues: 711
  sheet: -2.16 (0.30), residues: 280
  loop : -1.23 (0.18), residues: 1216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 346 
 TYR   0.012   0.001   TYR E 197 
 PHE   0.019   0.001   PHE A 105 
 TRP   0.007   0.001   TRP D 439 
 HIS   0.005   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (17471)
  covalent geometry    : angle       0.58739 (23543)
  hydrogen bonds       : bond        0.03934 (  570)
  hydrogen bonds       : angle       4.87522 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 118
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6929 (mtt) cc_final: 0.6408 (mtt)
REVERT: B   97 PHE cc_start: 0.8581 (t80) cc_final: 0.8365 (t80)
REVERT: B  161 MET cc_start: 0.1022 (mmm) cc_final: -0.0032 (mmp)
REVERT: B  256 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8758 (tp)
REVERT: D  131 TYR cc_start: 0.6265 (t80) cc_final: 0.5885 (t80)
REVERT: E  152 MET cc_start: 0.7621 (ttp) cc_final: 0.7361 (tmm)
REVERT: E  164 LYS cc_start: 0.8482 (tptt) cc_final: 0.8240 (tptt)
REVERT: F  114 MET cc_start: 0.0070 (tpt) cc_final: -0.2252 (mtm)
  outliers start: 66
  outliers final: 50
  residues processed: 177
  average time/residue: 0.1240
  time to fit residues: 35.3657
Evaluate side-chains
  161 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 110
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  342 ILE
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  182 LEU
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 218 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 106 optimal weight:    0.6980
   chunk 168 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 127 optimal weight:    8.9990
   chunk 170 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
B 329 GLN
C 329 GLN
E 100 GLN
F 266 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.151288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.108885 restraints weight = 35523.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.109070 restraints weight = 24326.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.109392 restraints weight = 18830.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.109759 restraints weight = 19344.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.110063 restraints weight = 17364.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17471  Z= 0.110
  Angle     :  0.543   9.445  23543  Z= 0.275
  Chirality :  0.045   0.187   2744
  Planarity :  0.004   0.047   2993
  Dihedral  :  4.671  45.372   2356
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.39 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.89 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.18), residues: 2207
  helix:  0.85 (0.20), residues: 723
  sheet: -2.16 (0.30), residues: 281
  loop : -1.18 (0.18), residues: 1203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 346 
 TYR   0.008   0.001   TYR F 197 
 PHE   0.016   0.001   PHE A 105 
 TRP   0.005   0.001   TRP B 439 
 HIS   0.004   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (17471)
  covalent geometry    : angle       0.54252 (23543)
  hydrogen bonds       : bond        0.03356 (  570)
  hydrogen bonds       : angle       4.54491 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 131
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6851 (mtt) cc_final: 0.6532 (mtt)
REVERT: B   97 PHE cc_start: 0.8624 (t80) cc_final: 0.8379 (t80)
REVERT: B  256 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8743 (tp)
REVERT: D  114 MET cc_start: 0.1795 (mmt) cc_final: 0.1225 (tpp)
REVERT: D  131 TYR cc_start: 0.6283 (t80) cc_final: 0.5914 (t80)
REVERT: D  164 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (tptp)
REVERT: D  239 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8376 (pp)
REVERT: E   61 TYR cc_start: 0.5805 (m-80) cc_final: 0.5477 (t80)
REVERT: E  152 MET cc_start: 0.7595 (ttp) cc_final: 0.7258 (tmm)
REVERT: E  164 LYS cc_start: 0.8420 (tptt) cc_final: 0.8182 (tptt)
REVERT: F  114 MET cc_start: -0.0049 (OUTLIER) cc_final: -0.2314 (mtm)
REVERT: F  152 MET cc_start: 0.3842 (tpt) cc_final: 0.2425 (tmm)
  outliers start: 62
  outliers final: 43
  residues processed: 181
  average time/residue: 0.1232
  time to fit residues: 35.1096
Evaluate side-chains
  165 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 118
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  376 ASN
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  329 GLN
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  164 LYS
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue  114 MET
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 163 optimal weight:    2.9990
   chunk 160 optimal weight:    0.4980
   chunk 217 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 197 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 157 optimal weight:    5.9990
   chunk 149 optimal weight:    0.7980
   chunk 42 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0270
   overall best weight:    1.2642

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
B 329 GLN
B 424 ASN
C 329 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.150850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.108129 restraints weight = 35303.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.107668 restraints weight = 26475.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.108162 restraints weight = 21327.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.108703 restraints weight = 19049.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.108919 restraints weight = 18137.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  17471  Z= 0.122
  Angle     :  0.546   9.331  23543  Z= 0.277
  Chirality :  0.045   0.171   2744
  Planarity :  0.004   0.044   2993
  Dihedral  :  4.623  47.202   2356
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.39 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.52 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.18), residues: 2207
  helix:  0.89 (0.20), residues: 723
  sheet: -2.15 (0.30), residues: 289
  loop : -1.17 (0.18), residues: 1195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 346 
 TYR   0.020   0.001   TYR E 208 
 PHE   0.015   0.001   PHE A 105 
 TRP   0.006   0.001   TRP D 439 
 HIS   0.004   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (17471)
  covalent geometry    : angle       0.54633 (23543)
  hydrogen bonds       : bond        0.03416 (  570)
  hydrogen bonds       : angle       4.51702 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 124
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  161 MET cc_start: 0.1270 (mmm) cc_final: 0.0364 (mmp)
REVERT: B  256 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: C  247 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8285 (tt)
REVERT: D  114 MET cc_start: 0.1809 (mmt) cc_final: 0.1227 (tpp)
REVERT: D  131 TYR cc_start: 0.6341 (t80) cc_final: 0.5965 (t80)
REVERT: D  164 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8336 (tptp)
REVERT: D  239 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8378 (pp)
REVERT: E   61 TYR cc_start: 0.5800 (m-80) cc_final: 0.5477 (t80)
REVERT: E  164 LYS cc_start: 0.8465 (tptt) cc_final: 0.8257 (tptt)
REVERT: F  114 MET cc_start: -0.0039 (OUTLIER) cc_final: -0.2326 (mtm)
REVERT: F  152 MET cc_start: 0.3770 (tpt) cc_final: 0.2344 (tmm)
  outliers start: 63
  outliers final: 43
  residues processed: 181
  average time/residue: 0.1110
  time to fit residues: 31.6105
Evaluate side-chains
  163 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 115
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  164 LYS
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  334 VAL
Chi-restraints excluded: chain E residue  342 ILE
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  114 MET
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 149 optimal weight:    1.9990
   chunk 150 optimal weight:    6.9990
   chunk 112 optimal weight:    0.7980
   chunk 110 optimal weight:    2.9990
   chunk 143 optimal weight:   20.0000
   chunk 119 optimal weight:    9.9990
   chunk 181 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
B 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.153366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.109365 restraints weight = 36253.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.112480 restraints weight = 25198.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.113717 restraints weight = 17402.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.113544 restraints weight = 16508.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113834 restraints weight = 16087.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  17471  Z= 0.127
  Angle     :  0.559   9.131  23543  Z= 0.281
  Chirality :  0.045   0.190   2744
  Planarity :  0.004   0.044   2993
  Dihedral  :  4.617  48.535   2355
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.75 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.78 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.18), residues: 2207
  helix:  0.95 (0.20), residues: 717
  sheet: -2.07 (0.30), residues: 280
  loop : -1.19 (0.18), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 240 
 TYR   0.019   0.001   TYR E 131 
 PHE   0.016   0.001   PHE B 323 
 TRP   0.006   0.001   TRP D 439 
 HIS   0.004   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (17471)
  covalent geometry    : angle       0.55875 (23543)
  hydrogen bonds       : bond        0.03401 (  570)
  hydrogen bonds       : angle       4.48074 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 120
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7016 (mtt) cc_final: 0.6728 (mtp)
REVERT: B  161 MET cc_start: 0.1114 (mmm) cc_final: 0.0254 (mmp)
REVERT: B  256 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: D  114 MET cc_start: 0.2047 (mmt) cc_final: 0.1407 (tpp)
REVERT: D  131 TYR cc_start: 0.6493 (t80) cc_final: 0.6127 (t80)
REVERT: D  239 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8373 (pp)
REVERT: E   61 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5443 (t80)
REVERT: E  152 MET cc_start: 0.7544 (ttp) cc_final: 0.7165 (tmm)
REVERT: E  164 LYS cc_start: 0.8487 (tptt) cc_final: 0.8275 (tptt)
REVERT: F  114 MET cc_start: -0.0045 (OUTLIER) cc_final: -0.2366 (mtm)
REVERT: F  152 MET cc_start: 0.3690 (tpt) cc_final: 0.2286 (tmm)
  outliers start: 60
  outliers final: 46
  residues processed: 173
  average time/residue: 0.1179
  time to fit residues: 32.6196
Evaluate side-chains
  162 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 112
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  322 THR
Chi-restraints excluded: chain C residue  329 GLN
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain D residue  426 ASP
Chi-restraints excluded: chain E residue   61 TYR
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  334 VAL
Chi-restraints excluded: chain E residue  342 ILE
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  114 MET
Chi-restraints excluded: chain F residue  182 LEU
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 216 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0370
   chunk 29 optimal weight:    3.9990
   chunk 182 optimal weight:    0.7980
   chunk 78 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 201 optimal weight:    7.9990
   chunk 161 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 180 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.1664

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 329 GLN
B 329 GLN
F 266 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.149437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104564 restraints weight = 35440.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106271 restraints weight = 26843.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.106587 restraints weight = 19188.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.106749 restraints weight = 19571.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.106979 restraints weight = 18524.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  17471  Z= 0.172
  Angle     :  0.602  13.957  23543  Z= 0.302
  Chirality :  0.047   0.162   2744
  Planarity :  0.004   0.043   2993
  Dihedral  :  4.800  48.357   2355
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.29 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.09 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.18), residues: 2207
  helix:  0.87 (0.20), residues: 707
  sheet: -1.99 (0.30), residues: 291
  loop : -1.22 (0.18), residues: 1209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 240 
 TYR   0.023   0.001   TYR E 131 
 PHE   0.017   0.001   PHE B 323 
 TRP   0.007   0.001   TRP D 439 
 HIS   0.005   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (17471)
  covalent geometry    : angle       0.60151 (23543)
  hydrogen bonds       : bond        0.03791 (  570)
  hydrogen bonds       : angle       4.60694 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 114
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7182 (mtt) cc_final: 0.6939 (mtp)
REVERT: A  422 MET cc_start: 0.7893 (ptp) cc_final: 0.7535 (ptp)
REVERT: B   97 PHE cc_start: 0.8447 (t80) cc_final: 0.8199 (t80)
REVERT: B  161 MET cc_start: 0.1068 (mmm) cc_final: 0.0412 (mmp)
REVERT: B  256 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8780 (tp)
REVERT: D  114 MET cc_start: 0.2121 (mmt) cc_final: 0.1479 (tpp)
REVERT: D  131 TYR cc_start: 0.6527 (t80) cc_final: 0.6148 (t80)
REVERT: D  239 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8509 (pp)
REVERT: E  152 MET cc_start: 0.7679 (ttp) cc_final: 0.7364 (tmm)
REVERT: E  164 LYS cc_start: 0.8531 (tptt) cc_final: 0.8326 (tptt)
REVERT: F  114 MET cc_start: -0.0083 (OUTLIER) cc_final: -0.2612 (mtm)
REVERT: F  152 MET cc_start: 0.3759 (tpt) cc_final: 0.2377 (tmm)
  outliers start: 58
  outliers final: 44
  residues processed: 165
  average time/residue: 0.1156
  time to fit residues: 30.6372
Evaluate side-chains
  159 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 112
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain D residue  426 ASP
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  141 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  204 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  334 VAL
Chi-restraints excluded: chain E residue  342 ILE
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain E residue  376 ASN
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   62 VAL
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  114 MET
Chi-restraints excluded: chain F residue  342 ILE
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 166 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0000
   chunk 22 optimal weight:    5.9990
   chunk 190 optimal weight:    0.0470
   chunk 187 optimal weight:    6.9990
   chunk 193 optimal weight:    4.9990
   chunk 172 optimal weight:    0.9980
   overall best weight:    0.5282

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
F 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.154859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.111948 restraints weight = 36335.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.113511 restraints weight = 25129.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.114709 restraints weight = 20162.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.115642 restraints weight = 16862.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.115747 restraints weight = 14933.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
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      :  0.002   0.039  17471  Z= 0.099
  Angle     :  0.554  14.056  23543  Z= 0.276
  Chirality :  0.045   0.175   2744
  Planarity :  0.004   0.044   2993
  Dihedral  :  4.573  50.736   2355
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.57 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.98 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.18), residues: 2207
  helix:  1.05 (0.20), residues: 714
  sheet: -2.08 (0.31), residues: 269
  loop : -1.16 (0.18), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 314 
 TYR   0.022   0.001   TYR E 131 
 PHE   0.017   0.001   PHE D  97 
 TRP   0.007   0.001   TRP B 439 
 HIS   0.003   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (17471)
  covalent geometry    : angle       0.55402 (23543)
  hydrogen bonds       : bond        0.03122 (  570)
  hydrogen bonds       : angle       4.29371 ( 1632)

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

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

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4414 Ramachandran restraints generated.
    2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 PHE cc_start: 0.8426 (t80) cc_final: 0.8210 (t80)
REVERT: B  161 MET cc_start: 0.1011 (mmm) cc_final: 0.0438 (mmp)
REVERT: B  256 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8745 (tp)
REVERT: D  114 MET cc_start: 0.2286 (mmt) cc_final: 0.1585 (tpp)
REVERT: D  131 TYR cc_start: 0.6669 (t80) cc_final: 0.6304 (t80)
REVERT: D  164 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8357 (pttm)
REVERT: D  239 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8305 (pp)
REVERT: D  263 LEU cc_start: 0.5304 (pp) cc_final: 0.5023 (mt)
REVERT: E  164 LYS cc_start: 0.8504 (tptt) cc_final: 0.8299 (tptt)
REVERT: E  170 GLN cc_start: 0.8145 (tt0) cc_final: 0.7924 (tt0)
REVERT: F  114 MET cc_start: 0.0115 (OUTLIER) cc_final: -0.2280 (mtm)
REVERT: F  152 MET cc_start: 0.3530 (tpt) cc_final: 0.2138 (tmm)
  outliers start: 40
  outliers final: 33
  residues processed: 162
  average time/residue: 0.1081
  time to fit residues: 28.3540
Evaluate side-chains
  159 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  329 GLN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   62 VAL
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  164 LYS
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  334 VAL
Chi-restraints excluded: chain D residue  371 VAL
Chi-restraints excluded: chain E residue   63 ASP
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  334 VAL
Chi-restraints excluded: chain E residue  355 ILE
Chi-restraints excluded: chain E residue  365 VAL
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   71 MET
Chi-restraints excluded: chain F residue  114 MET
Chi-restraints excluded: chain F residue  434 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 138 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0000
   chunk 163 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 171 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
** F  98 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 = 0.4241 r_free = 0.4241 target = 0.153803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.112340 restraints weight = 36398.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113613 restraints weight = 24158.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.113651 restraints weight = 18759.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.114294 restraints weight = 19171.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.114283 restraints weight = 17399.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  17471  Z= 0.121
  Angle     :  0.574  13.832  23543  Z= 0.286
  Chirality :  0.045   0.157   2744
  Planarity :  0.004   0.043   2993
  Dihedral  :  4.592  50.136   2355
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.43 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.45 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.18), residues: 2207
  helix:  1.12 (0.20), residues: 708
  sheet: -2.07 (0.31), residues: 269
  loop : -1.13 (0.18), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 346 
 TYR   0.019   0.001   TYR E 131 
 PHE   0.018   0.001   PHE B 323 
 TRP   0.005   0.001   TRP D 439 
 HIS   0.003   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (17471)
  covalent geometry    : angle       0.57442 (23543)
  hydrogen bonds       : bond        0.03319 (  570)
  hydrogen bonds       : angle       4.33742 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2669.61 seconds
wall clock time: 47 minutes 2.73 seconds (2822.73 seconds total)