Starting phenix.real_space_refine
on Wed Mar  4 07:21:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u23_26306/03_2026/7u23_26306.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
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      98      5.16       5
     C    7375      2.51       5
     N    2039      2.21       5
     O    2176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11688
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5380
          Classifications: {'peptide': 669}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5380
          Classifications: {'peptide': 669}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 464
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
    Chain: "D"
      Number of atoms: 464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 464
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
  Time building chain proxies: 2.58, per 1000 atoms: 0.22
  Number of scatterers: 11688
  At special positions: 0
  Unit cell: (107.06, 126.14, 149.46, 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      98     16.00
     O    2176      8.00
     N    2039      7.00
     C    7375      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=38, symmetry=0
    Simple disulfide: pdb=" SG  CYS E   3 " - pdb=" SG  CYS E  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 120 " - pdb=" SG  CYS E 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 152 " - pdb=" SG  CYS E 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 162 " - pdb=" SG  CYS E 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 185 " - pdb=" SG  CYS E 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 189 " - pdb=" SG  CYS E 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 201 " - pdb=" SG  CYS E 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 205 " - pdb=" SG  CYS E 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 221 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 234 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 252 " - pdb=" SG  CYS E 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 277 " - pdb=" SG  CYS E 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 294 " - pdb=" SG  CYS E 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 302 " - pdb=" SG  CYS E 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 425 " - pdb=" SG  CYS E 458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 776 " - pdb=" SG  CYS E 785 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   3 " - pdb=" SG  CYS F  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 120 " - pdb=" SG  CYS F 148 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 152 " - pdb=" SG  CYS F 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 162 " - pdb=" SG  CYS F 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 185 " - pdb=" SG  CYS F 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 189 " - pdb=" SG  CYS F 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 201 " - pdb=" SG  CYS F 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 205 " - pdb=" SG  CYS F 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 221 " - pdb=" SG  CYS F 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 234 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 252 " - pdb=" SG  CYS F 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 277 " - pdb=" SG  CYS F 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 294 " - pdb=" SG  CYS F 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 302 " - pdb=" SG  CYS F 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 425 " - pdb=" SG  CYS F 458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 776 " - pdb=" SG  CYS F 785 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  47 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  46 " - pdb=" SG  CYS D  52 " distance=2.03

  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: 0.84
  Conformation dependent library (CDL) restraints added in 562.6 milliseconds
  

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2764

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 28 sheets defined
      15.6% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'E' and resid 13 through 20
    Processing helix  chain 'E' and resid 65 through 69
    Processing helix  chain 'E' and resid 126 through 130
    Processing helix  chain 'E' and resid 133 through 137
    Processing helix  chain 'E' and resid 144 through 148
    Processing helix  chain 'E' and resid 249 through 253
    Processing helix  chain 'E' and resid 315 through 321
      removed outlier: 3.748A  pdb=" N   MET E 319 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 349
    Processing helix  chain 'E' and resid 425 through 437
      removed outlier: 3.783A  pdb=" N   ILE E 429 " --> pdb=" O   CYS E 425 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU E 434 " --> pdb=" O   TYR E 430 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL E 435 " --> pdb=" O   ARG E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 685 through 701
      removed outlier: 3.760A  pdb=" N   PHE E 701 " --> pdb=" O   HIS E 697 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 779 through 784
    Processing helix  chain 'F' and resid 13 through 20
    Processing helix  chain 'F' and resid 65 through 69
    Processing helix  chain 'F' and resid 144 through 148
    Processing helix  chain 'F' and resid 249 through 253
    Processing helix  chain 'F' and resid 315 through 321
      removed outlier: 3.756A  pdb=" N   MET F 319 " --> pdb=" O   SER F 316 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 340 through 348
      removed outlier: 3.533A  pdb=" N   GLU F 345 " --> pdb=" O   ALA F 341 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN F 346 " --> pdb=" O   SER F 342 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 349 through 351
      No H-bonds generated for 'chain 'F' and resid 349 through 351'
    Processing helix  chain 'F' and resid 425 through 437
      removed outlier: 3.865A  pdb=" N   ILE F 429 " --> pdb=" O   CYS F 425 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU F 434 " --> pdb=" O   TYR F 430 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL F 435 " --> pdb=" O   ARG F 431 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 684 through 701
      removed outlier: 3.736A  pdb=" N   PHE F 701 " --> pdb=" O   HIS F 697 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 779 through 782
    Processing helix  chain 'C' and resid 7 through 20
      removed outlier: 3.572A  pdb=" N   VAL C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 48
    Processing helix  chain 'C' and resid 53 through 61
    Processing helix  chain 'D' and resid 7 through 20
    Processing helix  chain 'D' and resid 21 through 23
      No H-bonds generated for 'chain 'D' and resid 21 through 23'
    Processing helix  chain 'D' and resid 41 through 48
      removed outlier: 3.717A  pdb=" N   CYS D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
    Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3
    Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 10
      removed outlier: 6.285A  pdb=" N   LEU E  29 " --> pdb=" O   LEU E  56 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE E  58 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE E  31 " --> pdb=" O   PHE E  58 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   VAL E  60 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   LEU E  33 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TYR E  85 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ARG E 112 " --> pdb=" O   TYR E  85 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU E  87 " --> pdb=" O   ARG E 112 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   GLU E 114 " --> pdb=" O   LEU E  87 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ILE E  89 " --> pdb=" O   GLU E 114 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE E 111 " --> pdb=" O   TYR E 138 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL E 140 " --> pdb=" O   ILE E 111 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE E 113 " --> pdb=" O   VAL E 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 164 through 167
      removed outlier: 3.724A  pdb=" N   THR E 165 " --> pdb=" O   ASN E 172 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 205 through 209
      removed outlier: 5.783A  pdb=" N   LEU E 206 " --> pdb=" O   CYS E 221 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   CYS E 221 " --> pdb=" O   LEU E 206 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   SER E 208 " --> pdb=" O   VAL E 219 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL E 219 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 224 through 226
    Processing sheet with id=AA6, first strand: chain 'E' and resid 245 through 248
      removed outlier: 3.840A  pdb=" N   ARG E 245 " --> pdb=" O   PHE E 241 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   CYS E 273 " --> pdb=" O   THR E 238 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ARG E 240 " --> pdb=" O   CYS E 273 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 282 through 283
    Processing sheet with id=AA8, first strand: chain 'E' and resid 302 through 311
      removed outlier: 10.962A  pdb=" N   ILE E 325 " --> pdb=" O   GLU E 303 " (cutoff:3.500A)
      removed outlier: 11.563A  pdb=" N   GLU E 305 " --> pdb=" O   ILE E 325 " (cutoff:3.500A)
      removed outlier: 10.564A  pdb=" N   LYS E 327 " --> pdb=" O   GLU E 305 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS E 307 " --> pdb=" O   LYS E 327 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 302 through 311
      removed outlier: 10.962A  pdb=" N   ILE E 325 " --> pdb=" O   GLU E 303 " (cutoff:3.500A)
      removed outlier: 11.563A  pdb=" N   GLU E 305 " --> pdb=" O   ILE E 325 " (cutoff:3.500A)
      removed outlier: 10.564A  pdb=" N   LYS E 327 " --> pdb=" O   GLU E 305 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS E 307 " --> pdb=" O   LYS E 327 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   TYR E 417 " --> pdb=" O   SER E 389 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   TYR E 391 " --> pdb=" O   TYR E 417 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ALA E 419 " --> pdb=" O   TYR E 391 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LEU E 393 " --> pdb=" O   ALA E 419 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 461 through 462
      removed outlier: 5.589A  pdb=" N   ASP E 461 " --> pdb=" O   LYS E 568 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 465 through 470
      removed outlier: 6.653A  pdb=" N   THR E 478 " --> pdb=" O   THR E 466 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR E 468 " --> pdb=" O   ILE E 476 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE E 476 " --> pdb=" O   THR E 468 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 520 through 525
    Processing sheet with id=AB4, first strand: chain 'E' and resid 585 through 590
      removed outlier: 4.522A  pdb=" N   VAL E 587 " --> pdb=" O   LYS E 600 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LYS E 600 " --> pdb=" O   VAL E 587 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER E 589 " --> pdb=" O   ILE E 598 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE E 598 " --> pdb=" O   SER E 589 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 747 through 752
      removed outlier: 4.279A  pdb=" N   TYR E 613 " --> pdb=" O   CYS E 776 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 2 through 3
    Processing sheet with id=AB7, first strand: chain 'F' and resid 6 through 10
      removed outlier: 6.325A  pdb=" N   LEU F  29 " --> pdb=" O   LEU F  56 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   PHE F  58 " --> pdb=" O   LEU F  29 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE F  31 " --> pdb=" O   PHE F  58 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   VAL F  60 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   LEU F  33 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG F 112 " --> pdb=" O   ALA F  86 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL F  88 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   GLU F 114 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE F  90 " --> pdb=" O   GLU F 114 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 164 through 167
      removed outlier: 3.749A  pdb=" N   THR F 165 " --> pdb=" O   ASN F 172 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 209
      removed outlier: 3.552A  pdb=" N   ALA F 220 " --> pdb=" O   LEU F 206 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   SER F 208 " --> pdb=" O   CYS F 218 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   CYS F 218 " --> pdb=" O   SER F 208 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226
    Processing sheet with id=AC2, first strand: chain 'F' and resid 245 through 248
      removed outlier: 3.791A  pdb=" N   ARG F 245 " --> pdb=" O   PHE F 241 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   CYS F 273 " --> pdb=" O   THR F 238 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ARG F 240 " --> pdb=" O   CYS F 273 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 282 through 283
    Processing sheet with id=AC4, first strand: chain 'F' and resid 301 through 311
      removed outlier: 11.033A  pdb=" N   ILE F 325 " --> pdb=" O   GLU F 303 " (cutoff:3.500A)
      removed outlier: 11.594A  pdb=" N   GLU F 305 " --> pdb=" O   ILE F 325 " (cutoff:3.500A)
      removed outlier: 10.554A  pdb=" N   LYS F 327 " --> pdb=" O   GLU F 305 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS F 307 " --> pdb=" O   LYS F 327 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 301 through 311
      removed outlier: 11.033A  pdb=" N   ILE F 325 " --> pdb=" O   GLU F 303 " (cutoff:3.500A)
      removed outlier: 11.594A  pdb=" N   GLU F 305 " --> pdb=" O   ILE F 325 " (cutoff:3.500A)
      removed outlier: 10.554A  pdb=" N   LYS F 327 " --> pdb=" O   GLU F 305 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS F 307 " --> pdb=" O   LYS F 327 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LYS F 415 " --> pdb=" O   TYR F 388 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA F 419 " --> pdb=" O   VAL F 392 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 461 through 463
      removed outlier: 5.640A  pdb=" N   ASP F 461 " --> pdb=" O   LYS F 568 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'F' and resid 465 through 470
      removed outlier: 6.622A  pdb=" N   THR F 478 " --> pdb=" O   THR F 466 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   THR F 468 " --> pdb=" O   ILE F 476 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ILE F 476 " --> pdb=" O   THR F 468 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 520 through 525
    Processing sheet with id=AC9, first strand: chain 'F' and resid 585 through 593
      removed outlier: 4.511A  pdb=" N   VAL F 587 " --> pdb=" O   LYS F 600 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LYS F 600 " --> pdb=" O   VAL F 587 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   SER F 589 " --> pdb=" O   ILE F 598 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE F 598 " --> pdb=" O   SER F 589 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   SER F 591 " --> pdb=" O   GLN F 596 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   GLN F 596 " --> pdb=" O   SER F 591 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 747 through 752
      removed outlier: 4.336A  pdb=" N   TYR F 613 " --> pdb=" O   CYS F 776 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3846
        1.34 -     1.46: 2774
        1.46 -     1.58: 5204
        1.58 -     1.70: 0
        1.70 -     1.83: 120
  Bond restraints: 11944
  Sorted by residual:
  bond pdb=" N   SER E 579 "
       pdb=" CA  SER E 579 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.15e-02 7.56e+03 7.57e+00
  bond pdb=" N   VAL E 580 "
       pdb=" CA  VAL E 580 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.23e-02 6.61e+03 6.80e+00
  bond pdb=" N   THR E 576 "
       pdb=" CA  THR E 576 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.25e-02 6.40e+03 6.45e+00
  bond pdb=" N   ASN E 577 "
       pdb=" CA  ASN E 577 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.031 1.31e-02 5.83e+03 5.51e+00
  bond pdb=" N   ALA E 578 "
       pdb=" CA  ALA E 578 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.023 1.28e-02 6.10e+03 3.35e+00
  ... (remaining 11939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 15499
        1.27 -     2.54: 543
        2.54 -     3.81: 139
        3.81 -     5.08: 12
        5.08 -     6.35: 4
  Bond angle restraints: 16197
  Sorted by residual:
  angle pdb=" N   ARG D  26 "
        pdb=" CA  ARG D  26 "
        pdb=" C   ARG D  26 "
      ideal   model   delta    sigma   weight residual
     110.73  117.08   -6.35 1.55e+00 4.16e-01 1.68e+01
  angle pdb=" CA  ARG D  26 "
        pdb=" C   ARG D  26 "
        pdb=" N   PRO D  27 "
      ideal   model   delta    sigma   weight residual
     117.84  121.27   -3.43 9.70e-01 1.06e+00 1.25e+01
  angle pdb=" C   THR E 107 "
        pdb=" N   ARG E 108 "
        pdb=" CA  ARG E 108 "
      ideal   model   delta    sigma   weight residual
     122.17  117.41    4.76 1.54e+00 4.22e-01 9.56e+00
  angle pdb=" CA  THR E 576 "
        pdb=" C   THR E 576 "
        pdb=" O   THR E 576 "
      ideal   model   delta    sigma   weight residual
     121.44  118.21    3.23 1.08e+00 8.57e-01 8.95e+00
  angle pdb=" CA  SER E 579 "
        pdb=" C   SER E 579 "
        pdb=" O   SER E 579 "
      ideal   model   delta    sigma   weight residual
     121.66  118.31    3.35 1.22e+00 6.72e-01 7.53e+00
  ... (remaining 16192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.40: 6649
       15.40 -    30.79: 479
       30.79 -    46.19: 134
       46.19 -    61.58: 42
       61.58 -    76.98: 9
  Dihedral angle restraints: 7313
    sinusoidal: 3033
      harmonic: 4280
  Sorted by residual:
  dihedral pdb=" CB  CYS C   7 "
           pdb=" SG  CYS C   7 "
           pdb=" SG  CYS C  47 "
           pdb=" CB  CYS C  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.41   70.41     1      1.00e+01 1.00e-02 6.38e+01
  dihedral pdb=" CB  CYS F 201 "
           pdb=" SG  CYS F 201 "
           pdb=" SG  CYS F 209 "
           pdb=" CB  CYS F 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.08  -52.08     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CB  CYS E 201 "
           pdb=" SG  CYS E 201 "
           pdb=" SG  CYS E 209 "
           pdb=" CB  CYS E 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.71  -51.71     1      1.00e+01 1.00e-02 3.65e+01
  ... (remaining 7310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1180
       0.033 -    0.067: 362
       0.067 -    0.100: 169
       0.100 -    0.133: 76
       0.133 -    0.166: 3
  Chirality restraints: 1790
  Sorted by residual:
  chirality pdb=" CA  VAL E 580 "
            pdb=" N   VAL E 580 "
            pdb=" C   VAL E 580 "
            pdb=" CB  VAL E 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CA  VAL C  24 "
            pdb=" N   VAL C  24 "
            pdb=" C   VAL C  24 "
            pdb=" CB  VAL C  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.04e-01
  chirality pdb=" CA  PRO E 422 "
            pdb=" N   PRO E 422 "
            pdb=" C   PRO E 422 "
            pdb=" CB  PRO E 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1787 not shown)

  Planarity restraints: 2091
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F   4 "   -0.047 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO F   5 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO F   5 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO F   5 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 143 "    0.038 5.00e-02 4.00e+02   5.72e-02 5.23e+00
        pdb=" N   PRO F 144 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO F 144 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO F 144 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS F 234 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO F 235 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO F 235 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F 235 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2088 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 924
        2.74 -     3.28: 11587
        3.28 -     3.82: 19134
        3.82 -     4.36: 23678
        4.36 -     4.90: 39111
  Nonbonded interactions: 94434
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 126 "
            pdb=" OG  SER E 128 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   LYS E 503 "
            pdb=" OH  TYR E 573 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   LYS F 503 "
            pdb=" OH  TYR F 573 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   PHE E 701 "
            pdb=" OH  TYR D  60 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD1 ASN E 698 "
            pdb=" N   GLY D  41 "
     model   vdw
     2.234 3.120
  ... (remaining 94429 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and (resid 1 through 256 or resid 265 through 798))
  selection = (chain 'F' and (resid 1 through 624 or resid 684 through 798))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.550
  Find NCS groups from input model:        0.170
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11982  Z= 0.199
  Angle     :  0.594   6.353  16273  Z= 0.329
  Chirality :  0.043   0.166   1790
  Planarity :  0.004   0.071   2091
  Dihedral  : 11.885  76.976   4435
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.73 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  :  6.79 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.20), residues: 1426
  helix: -1.46 (0.36), residues: 153
  sheet: -0.75 (0.30), residues: 289
  loop : -1.56 (0.18), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  26 
 TYR   0.012   0.001   TYR D  25 
 PHE   0.021   0.001   PHE F 692 
 TRP   0.013   0.001   TRP E  79 
 HIS   0.004   0.001   HIS F 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (11944)
  covalent geometry    : angle       0.59246 (16197)
  SS BOND              : bond        0.00276 (   38)
  SS BOND              : angle       0.92716 (   76)
  hydrogen bonds       : bond        0.26439 (  303)
  hydrogen bonds       : angle       9.94094 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 254
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7420 (mt) cc_final: 0.6849 (mt)
REVERT: E   85 TYR cc_start: 0.7734 (m-80) cc_final: 0.7531 (m-80)
REVERT: E  100 LEU cc_start: 0.9170 (mt) cc_final: 0.8716 (mt)
REVERT: E  169 ASN cc_start: 0.9159 (m-40) cc_final: 0.8858 (p0)
REVERT: E  398 LEU cc_start: 0.8993 (tp) cc_final: 0.8735 (tp)
REVERT: E  446 ASP cc_start: 0.6518 (m-30) cc_final: 0.6296 (m-30)
REVERT: F   76 ILE cc_start: 0.9039 (mt) cc_final: 0.8713 (tt)
REVERT: F  353 VAL cc_start: 0.8866 (t) cc_final: 0.8560 (t)
REVERT: F  398 LEU cc_start: 0.9277 (tp) cc_final: 0.9043 (tp)
REVERT: F  416 MET cc_start: 0.7559 (mtm) cc_final: 0.7230 (ptt)
REVERT: F  432 MET cc_start: 0.9004 (ttt) cc_final: 0.8455 (tmm)
REVERT: F  436 THR cc_start: 0.7987 (m) cc_final: 0.7436 (m)
REVERT: F  448 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (t0)
REVERT: F  490 LEU cc_start: 0.9315 (tt) cc_final: 0.9047 (mm)
REVERT: D   21 ASN cc_start: 0.7465 (m-40) cc_final: 0.7261 (p0)
  outliers start: 35
  outliers final: 9
  residues processed: 281
  average time/residue: 0.1229
  time to fit residues: 47.2046
Evaluate side-chains
  139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0060
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0670
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    1.5138

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

Flipped N/Q/H residues before XYZ refinement:
E  15 GLN
E 136 ASN
E 374 ASN
E 395 ASN
E 399 GLN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 694 ASN
F 374 ASN
F 399 GLN
F 621 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.082748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.062534 restraints weight = 82095.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.064506 restraints weight = 49908.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.065822 restraints weight = 34857.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.066720 restraints weight = 27015.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.067312 restraints weight = 22549.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11982  Z= 0.181
  Angle     :  0.699   9.701  16273  Z= 0.370
  Chirality :  0.048   0.204   1790
  Planarity :  0.005   0.062   2091
  Dihedral  :  5.239  25.593   1610
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.05 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.82 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.20), residues: 1426
  helix: -1.36 (0.35), residues: 170
  sheet: -0.58 (0.30), residues: 292
  loop : -1.41 (0.18), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  26 
 TYR   0.031   0.002   TYR E 496 
 PHE   0.024   0.002   PHE E 493 
 TRP   0.019   0.002   TRP E 402 
 HIS   0.006   0.001   HIS F 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (11944)
  covalent geometry    : angle       0.68097 (16197)
  SS BOND              : bond        0.01081 (   38)
  SS BOND              : angle       2.40743 (   76)
  hydrogen bonds       : bond        0.05376 (  303)
  hydrogen bonds       : angle       7.61678 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7609 (mt) cc_final: 0.7235 (mm)
REVERT: E   74 THR cc_start: 0.8738 (m) cc_final: 0.8480 (p)
REVERT: E  169 ASN cc_start: 0.8950 (m-40) cc_final: 0.8465 (p0)
REVERT: E  348 MET cc_start: 0.9056 (mpp) cc_final: 0.8724 (mpp)
REVERT: E  395 ASN cc_start: 0.8818 (m110) cc_final: 0.8455 (m-40)
REVERT: F   19 LEU cc_start: 0.9053 (mt) cc_final: 0.8837 (tt)
REVERT: F  366 LEU cc_start: 0.8743 (mm) cc_final: 0.8440 (mm)
REVERT: F  398 LEU cc_start: 0.9539 (tp) cc_final: 0.9267 (tp)
REVERT: F  401 LEU cc_start: 0.9214 (mm) cc_final: 0.8588 (tp)
REVERT: F  432 MET cc_start: 0.9155 (ttt) cc_final: 0.8695 (tmm)
REVERT: F  436 THR cc_start: 0.8291 (m) cc_final: 0.7570 (m)
REVERT: F  473 ASN cc_start: 0.9007 (p0) cc_final: 0.8723 (p0)
REVERT: F  521 MET cc_start: 0.8096 (mmp) cc_final: 0.7752 (mmm)
REVERT: F  529 ASN cc_start: 0.8677 (t0) cc_final: 0.8247 (t0)
REVERT: F  790 PHE cc_start: 0.8897 (p90) cc_final: 0.8616 (p90)
REVERT: C   36 ARG cc_start: 0.7802 (pmt170) cc_final: 0.7556 (mpp-170)
REVERT: D   36 ARG cc_start: 0.7584 (tmt170) cc_final: 0.7328 (mmt180)
REVERT: D   37 ASN cc_start: 0.8766 (p0) cc_final: 0.8473 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1198
  time to fit residues: 28.2011
Evaluate side-chains
  111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 136 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 138 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9980
   chunk 123 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 141 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
E  21 ASN
E 237 ASN
E 387 ASN
E 400 GLN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 179 ASN
** F 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.075045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.053830 restraints weight = 94428.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.055214 restraints weight = 62503.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.056080 restraints weight = 46852.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.056697 restraints weight = 38468.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.057150 restraints weight = 33588.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.108  11982  Z= 0.387
  Angle     :  1.014  13.855  16273  Z= 0.518
  Chirality :  0.053   0.177   1790
  Planarity :  0.007   0.065   2091
  Dihedral  :  6.607  35.508   1610
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 29.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.29 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.25 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -1.80 (0.21), residues: 1426
  helix: -1.04 (0.38), residues: 153
  sheet: -0.76 (0.29), residues: 309
  loop : -1.42 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 336 
 TYR   0.027   0.003   TYR F 497 
 PHE   0.033   0.004   PHE E 420 
 TRP   0.023   0.003   TRP F 519 
 HIS   0.011   0.003   HIS F 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00831 (11944)
  covalent geometry    : angle       1.00215 (16197)
  SS BOND              : bond        0.01069 (   38)
  SS BOND              : angle       2.48111 (   76)
  hydrogen bonds       : bond        0.05811 (  303)
  hydrogen bonds       : angle       7.97459 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7800 (mt) cc_final: 0.7549 (mm)
REVERT: E   93 THR cc_start: 0.5036 (OUTLIER) cc_final: 0.4676 (p)
REVERT: E  169 ASN cc_start: 0.9048 (m-40) cc_final: 0.8491 (p0)
REVERT: E  274 MET cc_start: 0.9007 (mpp) cc_final: 0.8788 (mpp)
REVERT: E  348 MET cc_start: 0.8562 (mpp) cc_final: 0.8209 (mpp)
REVERT: E  398 LEU cc_start: 0.9177 (tp) cc_final: 0.8962 (tp)
REVERT: E  521 MET cc_start: 0.4058 (mmt) cc_final: 0.3707 (mmt)
REVERT: F  344 LEU cc_start: 0.9836 (mt) cc_final: 0.9609 (mt)
REVERT: F  348 MET cc_start: 0.8958 (mpp) cc_final: 0.8690 (mpp)
REVERT: F  416 MET cc_start: 0.8448 (ptt) cc_final: 0.7627 (ptt)
REVERT: F  432 MET cc_start: 0.9013 (ttt) cc_final: 0.8595 (tmm)
REVERT: F  529 ASN cc_start: 0.8843 (t0) cc_final: 0.8321 (t0)
REVERT: F  760 ILE cc_start: 0.8994 (mm) cc_final: 0.8785 (tp)
REVERT: F  790 PHE cc_start: 0.9110 (p90) cc_final: 0.8908 (p90)
REVERT: F  796 MET cc_start: 0.8478 (mmp) cc_final: 0.8163 (mmm)
REVERT: C   62 ASN cc_start: 0.5611 (OUTLIER) cc_final: 0.4902 (m110)
REVERT: D   36 ARG cc_start: 0.7794 (tmt170) cc_final: 0.7278 (mmt180)
REVERT: D   37 ASN cc_start: 0.8885 (p0) cc_final: 0.8604 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 133
  average time/residue: 0.1045
  time to fit residues: 20.1927
Evaluate side-chains
  89 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 136 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** E  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 116 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 179 ASN
F 374 ASN
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.078701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.057694 restraints weight = 92784.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.059193 restraints weight = 60075.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.060212 restraints weight = 44329.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.060925 restraints weight = 35961.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.061349 restraints weight = 31244.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  11982  Z= 0.149
  Angle     :  0.660   8.146  16273  Z= 0.348
  Chirality :  0.048   0.241   1790
  Planarity :  0.005   0.042   2091
  Dihedral  :  5.768  26.469   1610
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.82 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.21), residues: 1426
  helix: -0.37 (0.41), residues: 148
  sheet: -0.65 (0.29), residues: 310
  loop : -1.26 (0.19), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 112 
 TYR   0.019   0.002   TYR F 547 
 PHE   0.021   0.002   PHE E 692 
 TRP   0.014   0.002   TRP F 519 
 HIS   0.006   0.001   HIS F 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11944)
  covalent geometry    : angle       0.64958 (16197)
  SS BOND              : bond        0.00440 (   38)
  SS BOND              : angle       1.83444 (   76)
  hydrogen bonds       : bond        0.04070 (  303)
  hydrogen bonds       : angle       7.10550 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: E   74 THR cc_start: 0.8730 (m) cc_final: 0.8352 (p)
REVERT: E  274 MET cc_start: 0.8973 (mpp) cc_final: 0.8745 (mpp)
REVERT: E  348 MET cc_start: 0.8649 (mpp) cc_final: 0.8176 (mpp)
REVERT: E  521 MET cc_start: 0.5169 (mpp) cc_final: 0.4820 (mpp)
REVERT: F   25 ILE cc_start: 0.8666 (tt) cc_final: 0.8027 (tp)
REVERT: F   76 ILE cc_start: 0.9255 (mt) cc_final: 0.8989 (tt)
REVERT: F  348 MET cc_start: 0.8824 (mpp) cc_final: 0.8602 (mpp)
REVERT: F  398 LEU cc_start: 0.9411 (mm) cc_final: 0.9133 (mm)
REVERT: F  416 MET cc_start: 0.8286 (ptt) cc_final: 0.7990 (ptt)
REVERT: F  432 MET cc_start: 0.8993 (ttt) cc_final: 0.8598 (tmm)
REVERT: F  473 ASN cc_start: 0.8924 (p0) cc_final: 0.8383 (t0)
REVERT: F  529 ASN cc_start: 0.8795 (t0) cc_final: 0.8251 (t0)
REVERT: F  760 ILE cc_start: 0.8989 (mm) cc_final: 0.8746 (tp)
REVERT: F  796 MET cc_start: 0.8593 (mmp) cc_final: 0.8388 (mmm)
REVERT: C   36 ARG cc_start: 0.7965 (pmt170) cc_final: 0.7755 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1044
  time to fit residues: 20.5185
Evaluate side-chains
  86 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 19 optimal weight:    0.0370
   chunk 46 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:    0.3980
   chunk 114 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   chunk 143 optimal weight:    9.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
E  11 ASN
** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.080633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.060044 restraints weight = 91394.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.061708 restraints weight = 57670.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.062815 restraints weight = 41545.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.063412 restraints weight = 33212.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.063902 restraints weight = 28761.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.5294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11982  Z= 0.118
  Angle     :  0.598   7.144  16273  Z= 0.318
  Chirality :  0.046   0.161   1790
  Planarity :  0.004   0.044   2091
  Dihedral  :  5.292  25.259   1610
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.10 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.22), residues: 1426
  helix: -0.37 (0.41), residues: 159
  sheet: -0.48 (0.30), residues: 311
  loop : -1.05 (0.20), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 689 
 TYR   0.014   0.001   TYR E 224 
 PHE   0.015   0.001   PHE E 692 
 TRP   0.011   0.001   TRP F 618 
 HIS   0.003   0.001   HIS E  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (11944)
  covalent geometry    : angle       0.59018 (16197)
  SS BOND              : bond        0.00239 (   38)
  SS BOND              : angle       1.55580 (   76)
  hydrogen bonds       : bond        0.03642 (  303)
  hydrogen bonds       : angle       6.77428 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: E   74 THR cc_start: 0.8648 (m) cc_final: 0.8331 (p)
REVERT: E   92 MET cc_start: 0.7131 (ttt) cc_final: 0.6457 (tmm)
REVERT: E   95 LEU cc_start: 0.9163 (tp) cc_final: 0.8078 (tp)
REVERT: E  348 MET cc_start: 0.8728 (mpp) cc_final: 0.8190 (mpp)
REVERT: F   76 ILE cc_start: 0.9460 (mt) cc_final: 0.9193 (tt)
REVERT: F  344 LEU cc_start: 0.9635 (mt) cc_final: 0.9288 (mt)
REVERT: F  348 MET cc_start: 0.8793 (mpp) cc_final: 0.8522 (mpp)
REVERT: F  398 LEU cc_start: 0.9503 (mm) cc_final: 0.9173 (mm)
REVERT: F  400 GLN cc_start: 0.9233 (pm20) cc_final: 0.8995 (pm20)
REVERT: F  416 MET cc_start: 0.8276 (ptt) cc_final: 0.7738 (ptt)
REVERT: F  432 MET cc_start: 0.9009 (ttt) cc_final: 0.8540 (tmm)
REVERT: F  436 THR cc_start: 0.8443 (m) cc_final: 0.7707 (p)
REVERT: F  473 ASN cc_start: 0.8759 (p0) cc_final: 0.8343 (t0)
REVERT: F  529 ASN cc_start: 0.8807 (t0) cc_final: 0.8243 (t0)
REVERT: F  796 MET cc_start: 0.8598 (mmp) cc_final: 0.8387 (mmm)
REVERT: C   33 ARG cc_start: 0.7771 (tpt90) cc_final: 0.7358 (mtt-85)
REVERT: D    5 ILE cc_start: 0.8465 (mp) cc_final: 0.8216 (mm)
REVERT: D   37 ASN cc_start: 0.8930 (p0) cc_final: 0.8726 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1061
  time to fit residues: 21.7400
Evaluate side-chains
  91 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 137 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 53 optimal weight:   20.0000
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
E  15 GLN
E 395 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 172 ASN
F 374 ASN
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.079954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.061398 restraints weight = 91870.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.062012 restraints weight = 67050.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.062497 restraints weight = 48985.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.062623 restraints weight = 44416.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.062735 restraints weight = 41703.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.5535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11982  Z= 0.127
  Angle     :  0.592   6.633  16273  Z= 0.313
  Chirality :  0.046   0.185   1790
  Planarity :  0.004   0.043   2091
  Dihedral  :  5.219  25.136   1610
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.68 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.22), residues: 1426
  helix: -0.32 (0.40), residues: 159
  sheet: -0.39 (0.30), residues: 311
  loop : -0.96 (0.21), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 112 
 TYR   0.014   0.001   TYR E 224 
 PHE   0.014   0.001   PHE E 692 
 TRP   0.028   0.001   TRP F 404 
 HIS   0.003   0.001   HIS F 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11944)
  covalent geometry    : angle       0.58428 (16197)
  SS BOND              : bond        0.00274 (   38)
  SS BOND              : angle       1.49576 (   76)
  hydrogen bonds       : bond        0.03434 (  303)
  hydrogen bonds       : angle       6.60476 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7797 (mt) cc_final: 0.7484 (mm)
REVERT: E   74 THR cc_start: 0.8880 (m) cc_final: 0.8574 (p)
REVERT: E   92 MET cc_start: 0.7077 (ttt) cc_final: 0.6761 (ttt)
REVERT: E   95 LEU cc_start: 0.9216 (tp) cc_final: 0.8695 (tp)
REVERT: E  348 MET cc_start: 0.8622 (mpp) cc_final: 0.8149 (mpp)
REVERT: E  436 THR cc_start: 0.6283 (m) cc_final: 0.5823 (p)
REVERT: F  398 LEU cc_start: 0.9513 (mm) cc_final: 0.9205 (mm)
REVERT: F  416 MET cc_start: 0.8287 (ptt) cc_final: 0.7815 (ptt)
REVERT: F  432 MET cc_start: 0.8865 (ttt) cc_final: 0.8445 (tmm)
REVERT: F  436 THR cc_start: 0.8496 (m) cc_final: 0.7716 (m)
REVERT: F  529 ASN cc_start: 0.8398 (t0) cc_final: 0.7981 (t0)
REVERT: F  796 MET cc_start: 0.8719 (mmp) cc_final: 0.8457 (mmp)
REVERT: C   33 ARG cc_start: 0.7931 (tpt90) cc_final: 0.7364 (mtt-85)
REVERT: D   37 ASN cc_start: 0.8943 (p0) cc_final: 0.8742 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0992
  time to fit residues: 18.4828
Evaluate side-chains
  90 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 125 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 ASN
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.079206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.058380 restraints weight = 91906.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.059933 restraints weight = 59921.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.061003 restraints weight = 43586.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.061709 restraints weight = 35239.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.062141 restraints weight = 30488.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.5710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11982  Z= 0.129
  Angle     :  0.592   8.808  16273  Z= 0.312
  Chirality :  0.046   0.166   1790
  Planarity :  0.004   0.056   2091
  Dihedral  :  5.183  25.154   1610
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.68 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.23), residues: 1426
  helix: -0.12 (0.42), residues: 152
  sheet: -0.29 (0.30), residues: 307
  loop : -0.90 (0.21), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  10 
 TYR   0.019   0.001   TYR D  25 
 PHE   0.013   0.001   PHE E 692 
 TRP   0.021   0.001   TRP F 404 
 HIS   0.003   0.001   HIS F 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11944)
  covalent geometry    : angle       0.58597 (16197)
  SS BOND              : bond        0.00246 (   38)
  SS BOND              : angle       1.38876 (   76)
  hydrogen bonds       : bond        0.03440 (  303)
  hydrogen bonds       : angle       6.54052 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7857 (mt) cc_final: 0.7590 (mm)
REVERT: E   74 THR cc_start: 0.8710 (m) cc_final: 0.8431 (p)
REVERT: E   92 MET cc_start: 0.6891 (ttt) cc_final: 0.6596 (ttt)
REVERT: E   95 LEU cc_start: 0.9139 (tp) cc_final: 0.8558 (tp)
REVERT: E  348 MET cc_start: 0.8763 (mpp) cc_final: 0.8428 (mpp)
REVERT: E  436 THR cc_start: 0.6138 (m) cc_final: 0.5689 (p)
REVERT: E  558 MET cc_start: 0.3926 (tpt) cc_final: 0.3311 (pmm)
REVERT: F  319 MET cc_start: 0.8361 (tmm) cc_final: 0.8126 (tmm)
REVERT: F  348 MET cc_start: 0.8719 (mmp) cc_final: 0.8497 (mmm)
REVERT: F  398 LEU cc_start: 0.9538 (mm) cc_final: 0.9210 (mm)
REVERT: F  416 MET cc_start: 0.8348 (ptt) cc_final: 0.7954 (ptt)
REVERT: F  436 THR cc_start: 0.8458 (m) cc_final: 0.7940 (p)
REVERT: F  529 ASN cc_start: 0.8844 (t0) cc_final: 0.8285 (t0)
REVERT: F  796 MET cc_start: 0.8725 (mmp) cc_final: 0.8429 (mmp)
REVERT: D    5 ILE cc_start: 0.8375 (mp) cc_final: 0.8119 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0920
  time to fit residues: 17.3786
Evaluate side-chains
  86 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 113 optimal weight:    8.9990
   chunk 141 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 109 optimal weight:    0.4980
   chunk 51 optimal weight:   10.0000
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.078812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.057776 restraints weight = 92226.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.059194 restraints weight = 59158.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.060161 restraints weight = 43478.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.060903 restraints weight = 35134.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.061203 restraints weight = 30313.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11982  Z= 0.148
  Angle     :  0.617   7.019  16273  Z= 0.325
  Chirality :  0.046   0.168   1790
  Planarity :  0.005   0.083   2091
  Dihedral  :  5.266  25.307   1610
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.52 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.22), residues: 1426
  helix: -0.13 (0.41), residues: 151
  sheet: -0.35 (0.30), residues: 307
  loop : -0.91 (0.21), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F 689 
 TYR   0.013   0.001   TYR E 224 
 PHE   0.020   0.002   PHE E  58 
 TRP   0.023   0.002   TRP F 404 
 HIS   0.005   0.001   HIS E 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11944)
  covalent geometry    : angle       0.60758 (16197)
  SS BOND              : bond        0.00275 (   38)
  SS BOND              : angle       1.67959 (   76)
  hydrogen bonds       : bond        0.03458 (  303)
  hydrogen bonds       : angle       6.55955 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7822 (mt) cc_final: 0.7588 (mm)
REVERT: E   53 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7679 (mm-30)
REVERT: E   74 THR cc_start: 0.8761 (m) cc_final: 0.8471 (p)
REVERT: E   95 LEU cc_start: 0.9192 (tp) cc_final: 0.8912 (tp)
REVERT: E  348 MET cc_start: 0.8736 (mpp) cc_final: 0.8409 (mpp)
REVERT: F  184 MET cc_start: 0.4115 (mtm) cc_final: 0.3809 (mtt)
REVERT: F  348 MET cc_start: 0.8696 (mmp) cc_final: 0.8378 (mmm)
REVERT: F  398 LEU cc_start: 0.9535 (mm) cc_final: 0.9229 (mm)
REVERT: F  432 MET cc_start: 0.8542 (ppp) cc_final: 0.8277 (ppp)
REVERT: F  760 ILE cc_start: 0.8805 (mm) cc_final: 0.8578 (tp)
REVERT: F  796 MET cc_start: 0.8772 (mmp) cc_final: 0.8481 (mmp)
REVERT: D   37 ASN cc_start: 0.8983 (p0) cc_final: 0.8758 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0943
  time to fit residues: 17.0442
Evaluate side-chains
  81 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0570
   chunk 73 optimal weight:    0.1980
   chunk 23 optimal weight:    2.9990
   chunk 141 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.6102

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 ASN
F 374 ASN
** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.076618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.055014 restraints weight = 86797.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.056755 restraints weight = 53457.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.057919 restraints weight = 38443.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.058721 restraints weight = 30559.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.059252 restraints weight = 26123.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11982  Z= 0.156
  Angle     :  0.618   7.181  16273  Z= 0.327
  Chirality :  0.046   0.172   1790
  Planarity :  0.005   0.067   2091
  Dihedral  :  5.318  24.189   1610
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.87 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.22), residues: 1426
  helix: -0.13 (0.42), residues: 145
  sheet: -0.48 (0.29), residues: 311
  loop : -0.85 (0.21), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 689 
 TYR   0.013   0.001   TYR E 224 
 PHE   0.022   0.002   PHE E  90 
 TRP   0.023   0.002   TRP F 404 
 HIS   0.006   0.001   HIS E 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (11944)
  covalent geometry    : angle       0.61059 (16197)
  SS BOND              : bond        0.00305 (   38)
  SS BOND              : angle       1.56183 (   76)
  hydrogen bonds       : bond        0.03518 (  303)
  hydrogen bonds       : angle       6.60401 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7905 (mt) cc_final: 0.7689 (mm)
REVERT: E   74 THR cc_start: 0.8720 (m) cc_final: 0.8423 (p)
REVERT: E   92 MET cc_start: 0.7137 (ttt) cc_final: 0.6325 (tmm)
REVERT: E   95 LEU cc_start: 0.9160 (tp) cc_final: 0.8420 (tp)
REVERT: E  348 MET cc_start: 0.8600 (mpp) cc_final: 0.8307 (mpp)
REVERT: E  366 LEU cc_start: 0.9199 (mt) cc_final: 0.8841 (tp)
REVERT: E  558 MET cc_start: 0.4141 (tpt) cc_final: 0.3417 (pmm)
REVERT: F  184 MET cc_start: 0.4662 (mtm) cc_final: 0.4135 (mtm)
REVERT: F  331 LEU cc_start: 0.9161 (tt) cc_final: 0.8802 (mt)
REVERT: F  348 MET cc_start: 0.8924 (mmp) cc_final: 0.8559 (mmm)
REVERT: F  398 LEU cc_start: 0.9511 (mm) cc_final: 0.9185 (mm)
REVERT: F  760 ILE cc_start: 0.8863 (mm) cc_final: 0.8660 (tp)
REVERT: F  796 MET cc_start: 0.8752 (mmp) cc_final: 0.8476 (mmm)
REVERT: D   37 ASN cc_start: 0.9009 (p0) cc_final: 0.8785 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0965
  time to fit residues: 16.5523
Evaluate side-chains
  79 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0020
   chunk 106 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 64 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0070
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.3806

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

Flipped N/Q/H residues before XYZ refinement:
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN
** C  16 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 = 0.3952 r_free = 0.3952 target = 0.078202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.056393 restraints weight = 86822.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.058278 restraints weight = 52583.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.059547 restraints weight = 37366.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.060400 restraints weight = 29453.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.060967 restraints weight = 24939.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.6242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  11982  Z= 0.107
  Angle     :  0.585   7.201  16273  Z= 0.309
  Chirality :  0.046   0.172   1790
  Planarity :  0.004   0.052   2091
  Dihedral  :  5.106  24.512   1610
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.10 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.91 (0.23), residues: 1426
  helix: -0.10 (0.42), residues: 144
  sheet: -0.22 (0.31), residues: 299
  loop : -0.81 (0.21), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 689 
 TYR   0.013   0.001   TYR E 224 
 PHE   0.017   0.001   PHE E  58 
 TRP   0.020   0.001   TRP F 404 
 HIS   0.003   0.001   HIS F 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (11944)
  covalent geometry    : angle       0.57630 (16197)
  SS BOND              : bond        0.00257 (   38)
  SS BOND              : angle       1.57145 (   76)
  hydrogen bonds       : bond        0.03367 (  303)
  hydrogen bonds       : angle       6.45975 (  759)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   74 THR cc_start: 0.8574 (m) cc_final: 0.8313 (p)
REVERT: E   92 MET cc_start: 0.7068 (ttt) cc_final: 0.6444 (tmm)
REVERT: E   95 LEU cc_start: 0.9145 (tp) cc_final: 0.8365 (tp)
REVERT: E  348 MET cc_start: 0.8606 (mpp) cc_final: 0.8307 (mpp)
REVERT: E  558 MET cc_start: 0.4071 (tpt) cc_final: 0.3398 (pmm)
REVERT: F  331 LEU cc_start: 0.9225 (tt) cc_final: 0.8879 (mt)
REVERT: F  348 MET cc_start: 0.8687 (mmp) cc_final: 0.8381 (mmm)
REVERT: F  398 LEU cc_start: 0.9469 (mm) cc_final: 0.9127 (mm)
REVERT: F  796 MET cc_start: 0.8676 (mmp) cc_final: 0.8395 (mmp)
REVERT: D    5 ILE cc_start: 0.8306 (mp) cc_final: 0.8026 (mm)
REVERT: D   37 ASN cc_start: 0.8956 (p0) cc_final: 0.8743 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1064
  time to fit residues: 17.6527
Evaluate side-chains
  84 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 116 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0870
   chunk 53 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0670
   chunk 125 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.5900

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 451 ASN
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 ASN
** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 621 GLN
F 698 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.076489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.054668 restraints weight = 88140.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.056449 restraints weight = 54024.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.057641 restraints weight = 38678.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.058440 restraints weight = 30681.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.058986 restraints weight = 26237.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.6469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11982  Z= 0.158
  Angle     :  0.622   7.250  16273  Z= 0.327
  Chirality :  0.046   0.224   1790
  Planarity :  0.005   0.048   2091
  Dihedral  :  5.241  24.292   1610
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.59 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.46 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.84 (0.23), residues: 1426
  helix:  0.09 (0.43), residues: 138
  sheet: -0.31 (0.30), residues: 305
  loop : -0.73 (0.21), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 689 
 TYR   0.012   0.001   TYR E 224 
 PHE   0.020   0.002   PHE E  90 
 TRP   0.019   0.002   TRP F 404 
 HIS   0.007   0.001   HIS E 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (11944)
  covalent geometry    : angle       0.61392 (16197)
  SS BOND              : bond        0.00283 (   38)
  SS BOND              : angle       1.56488 (   76)
  hydrogen bonds       : bond        0.03395 (  303)
  hydrogen bonds       : angle       6.49547 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2492.07 seconds
wall clock time: 43 minutes 37.91 seconds (2617.91 seconds total)