Starting phenix.real_space_refine
on Sun Aug 24 06:39:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4c_41878/08_2025/8u4c_41878_neut.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3510 atoms to isotropic.
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     120      5.16       5
     C    9324      2.51       5
     N    2532      2.21       5
     O    2730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14706
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6610
          Classifications: {'peptide': 817}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 6610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6610
          Classifications: {'peptide': 817}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 323
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 420
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 2, 'TRANS': 51}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 323
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 420
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 2, 'TRANS': 51}
          Chain breaks: 1
  Time building chain proxies: 2.78, per 1000 atoms: 0.19
  Number of scatterers: 14706
  At special positions: 0
  Unit cell: (135, 122.04, 170.64, 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     120     16.00
     O    2730      8.00
     N    2532      7.00
     C    9324      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=46, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 647 " - pdb=" SG  CYS A 872 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 798 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS B 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 266 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 312 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 435 " - pdb=" SG  CYS B 468 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 647 " - pdb=" SG  CYS B 872 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 798 " - pdb=" SG  CYS B 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   9 " - pdb=" SG  CYS C  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  21 " - pdb=" SG  CYS C  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   9 " - pdb=" SG  CYS D  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  21 " - pdb=" SG  CYS D  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  46 " - pdb=" SG  CYS D  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   9 " - pdb=" SG  CYS E  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  46 " - pdb=" SG  CYS E  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   9 " - pdb=" SG  CYS F  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  21 " - pdb=" SG  CYS F  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  46 " - pdb=" SG  CYS F  51 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 604.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3432

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 30 sheets defined
      17.1% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 24
      removed outlier: 3.584A  pdb=" N   ARG A  19 " --> pdb=" O   ASN A  16 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLU A  22 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A  23 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 132 through 136
      removed outlier: 3.664A  pdb=" N   ARG A 135 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 143
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 4.243A  pdb=" N   ASN A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 225
      removed outlier: 3.650A  pdb=" N   CYS A 225 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 269
    Processing helix  chain 'A' and resid 323 through 329
      removed outlier: 3.893A  pdb=" N   GLU A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 358
    Processing helix  chain 'A' and resid 435 through 447
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 3.781A  pdb=" N   PHE A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU A 643 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 638 through 643'
    Processing helix  chain 'A' and resid 692 through 714
    Processing helix  chain 'A' and resid 874 through 881
    Processing helix  chain 'B' and resid 16 through 24
      removed outlier: 3.580A  pdb=" N   ARG B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   HIS B  21 " --> pdb=" O   THR B  18 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU B  22 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  23 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 132 through 136
      removed outlier: 3.663A  pdb=" N   ARG B 135 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 143
    Processing helix  chain 'B' and resid 148 through 153
      removed outlier: 4.250A  pdb=" N   ASN B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
      removed outlier: 3.657A  pdb=" N   CYS B 225 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 269
    Processing helix  chain 'B' and resid 323 through 329
      removed outlier: 3.900A  pdb=" N   GLU B 329 " --> pdb=" O   THR B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 358
    Processing helix  chain 'B' and resid 435 through 447
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 638 through 643
      removed outlier: 3.772A  pdb=" N   PHE B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLU B 643 " --> pdb=" O   SER B 639 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 638 through 643'
    Processing helix  chain 'B' and resid 692 through 714
      removed outlier: 3.562A  pdb=" N   LEU B 696 " --> pdb=" O   ILE B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 874 through 881
    Processing helix  chain 'C' and resid 13 through 22
      removed outlier: 3.518A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 60
      removed outlier: 3.805A  pdb=" N   THR C  58 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   CYS C  60 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 17
      removed outlier: 3.863A  pdb=" N   ASP D  15 " --> pdb=" O   GLY D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 47
    Processing helix  chain 'D' and resid 52 through 58
      removed outlier: 3.704A  pdb=" N   LEU D  56 " --> pdb=" O   ASP D  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 22
      removed outlier: 3.514A  pdb=" N   LEU E  17 " --> pdb=" O   LEU E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 60
      removed outlier: 3.803A  pdb=" N   THR E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   CYS E  60 " --> pdb=" O   LEU E  56 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 11 through 17
      removed outlier: 3.879A  pdb=" N   ASP F  15 " --> pdb=" O   GLY F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 47
    Processing helix  chain 'F' and resid 52 through 58
      removed outlier: 3.675A  pdb=" N   LEU F  56 " --> pdb=" O   ASP F  52 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
      removed outlier: 7.031A  pdb=" N   GLN A  34 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A  36 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ARG A  65 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   VAL A 117 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   VAL A 146 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE A 119 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
    Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248
    Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279
    Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293
      removed outlier: 3.625A  pdb=" N   THR A 302 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321
      removed outlier: 9.953A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 313 " (cutoff:3.500A)
      removed outlier: 10.734A  pdb=" N   LEU A 315 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 9.537A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLY A 317 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321
      removed outlier: 9.953A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 313 " (cutoff:3.500A)
      removed outlier: 10.734A  pdb=" N   LEU A 315 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 9.537A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLY A 317 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473
    Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 4.053A  pdb=" N   ARG A 479 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A 486 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 533
      removed outlier: 3.551A  pdb=" N   LEU A 505 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY A 502 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605
      removed outlier: 5.560A  pdb=" N   ASP A 600 " --> pdb=" O   LYS A 616 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   LYS A 616 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 771 through 774
      removed outlier: 3.666A  pdb=" N   GLU A 772 " --> pdb=" O   VAL A 630 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL A 630 " --> pdb=" O   GLU A 772 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS A 627 " --> pdb=" O   CYS A 798 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 827 through 834
      removed outlier: 5.092A  pdb=" N   GLN A 845 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   CYS A 884 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 863
      removed outlier: 3.724A  pdb=" N   GLY A 892 " --> pdb=" O   VAL A 917 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 917 " --> pdb=" O   GLY A 892 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13
      removed outlier: 7.031A  pdb=" N   GLN B  34 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B  63 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU B  36 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ARG B  65 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL B 117 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   VAL B 146 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE B 119 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29
    Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173
    Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248
    Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279
    Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293
      removed outlier: 3.624A  pdb=" N   THR B 302 " --> pdb=" O   THR B 293 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321
      removed outlier: 9.946A  pdb=" N   VAL B 335 " --> pdb=" O   HIS B 313 " (cutoff:3.500A)
      removed outlier: 10.729A  pdb=" N   LEU B 315 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 9.542A  pdb=" N   ASN B 337 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   GLY B 317 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321
      removed outlier: 9.946A  pdb=" N   VAL B 335 " --> pdb=" O   HIS B 313 " (cutoff:3.500A)
      removed outlier: 10.729A  pdb=" N   LEU B 315 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 9.542A  pdb=" N   ASN B 337 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   GLY B 317 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 473
    Processing sheet with id=AC7, first strand: chain 'B' and resid 479 through 480
      removed outlier: 4.001A  pdb=" N   ARG B 479 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 486 " --> pdb=" O   ARG B 479 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 530 through 533
      removed outlier: 3.501A  pdb=" N   THR B 530 " --> pdb=" O   TYR B 507 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 505 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 599 through 605
      removed outlier: 5.554A  pdb=" N   ASP B 600 " --> pdb=" O   LYS B 616 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   LYS B 616 " --> pdb=" O   ASP B 600 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 774
      removed outlier: 3.604A  pdb=" N   GLU B 772 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL B 630 " --> pdb=" O   GLU B 772 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 834
      removed outlier: 5.070A  pdb=" N   GLN B 845 " --> pdb=" O   PRO B 829 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 854 through 863
      removed outlier: 3.707A  pdb=" N   GLY B 892 " --> pdb=" O   VAL B 917 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL B 917 " --> pdb=" O   GLY B 892 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    861 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: 2.31

  Time building geometry restraints manager: 1.46 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: 4830
        1.34 -     1.46: 3439
        1.46 -     1.58: 6637
        1.58 -     1.70: 0
        1.70 -     1.82: 142
  Bond restraints: 15048
  Sorted by residual:
  bond pdb=" C   CYS A 192 "
       pdb=" N   PRO A 193 "
    ideal  model  delta    sigma   weight residual
    1.332  1.356 -0.025 1.33e-02 5.65e+03 3.41e+00
  bond pdb=" C   CYS B 192 "
       pdb=" N   PRO B 193 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.33e-02 5.65e+03 3.11e+00
  bond pdb=" CB  ARG F  38 "
       pdb=" CG  ARG F  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" CA  ARG D  38 "
       pdb=" CB  ARG D  38 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.59e-02 3.96e+03 1.15e+00
  bond pdb=" CB  ASP D  52 "
       pdb=" CG  ASP D  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.08e+00
  ... (remaining 15043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 20163
        2.43 -     4.87: 180
        4.87 -     7.30: 17
        7.30 -     9.74: 12
        9.74 -    12.17: 2
  Bond angle restraints: 20374
  Sorted by residual:
  angle pdb=" N   ILE A 692 "
        pdb=" CA  ILE A 692 "
        pdb=" C   ILE A 692 "
      ideal   model   delta    sigma   weight residual
     113.53  108.38    5.15 9.80e-01 1.04e+00 2.77e+01
  angle pdb=" CA  ARG F  38 "
        pdb=" CB  ARG F  38 "
        pdb=" CG  ARG F  38 "
      ideal   model   delta    sigma   weight residual
     114.10  123.50   -9.40 2.00e+00 2.50e-01 2.21e+01
  angle pdb=" CA  ARG D  38 "
        pdb=" CB  ARG D  38 "
        pdb=" CG  ARG D  38 "
      ideal   model   delta    sigma   weight residual
     114.10  123.12   -9.02 2.00e+00 2.50e-01 2.03e+01
  angle pdb=" CB  MET B 843 "
        pdb=" CG  MET B 843 "
        pdb=" SD  MET B 843 "
      ideal   model   delta    sigma   weight residual
     112.70  124.87  -12.17 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" CB  MET A 843 "
        pdb=" CG  MET A 843 "
        pdb=" SD  MET A 843 "
      ideal   model   delta    sigma   weight residual
     112.70  124.32  -11.62 3.00e+00 1.11e-01 1.50e+01
  ... (remaining 20369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 7713
       17.74 -    35.48: 1094
       35.48 -    53.22: 249
       53.22 -    70.96: 43
       70.96 -    88.70: 41
  Dihedral angle restraints: 9140
    sinusoidal: 3826
      harmonic: 5314
  Sorted by residual:
  dihedral pdb=" CB  CYS A 288 "
           pdb=" SG  CYS A 288 "
           pdb=" SG  CYS A 301 "
           pdb=" CB  CYS A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.73   84.73     1      1.00e+01 1.00e-02 8.72e+01
  dihedral pdb=" CB  CYS B 288 "
           pdb=" SG  CYS B 288 "
           pdb=" SG  CYS B 301 "
           pdb=" CB  CYS B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.51   84.51     1      1.00e+01 1.00e-02 8.68e+01
  dihedral pdb=" CB  CYS A 241 "
           pdb=" SG  CYS A 241 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.27   77.27     1      1.00e+01 1.00e-02 7.48e+01
  ... (remaining 9137 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1378
       0.031 -    0.061: 529
       0.061 -    0.092: 168
       0.092 -    0.122: 129
       0.122 -    0.153: 12
  Chirality restraints: 2216
  Sorted by residual:
  chirality pdb=" CA  THR B 802 "
            pdb=" N   THR B 802 "
            pdb=" C   THR B 802 "
            pdb=" CB  THR B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.83e-01
  chirality pdb=" CA  THR A 802 "
            pdb=" N   THR A 802 "
            pdb=" C   THR A 802 "
            pdb=" CB  THR A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.81e-01
  chirality pdb=" CA  ILE B 457 "
            pdb=" N   ILE B 457 "
            pdb=" C   ILE B 457 "
            pdb=" CB  ILE B 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 2213 not shown)

  Planarity restraints: 2634
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 632 "    0.017 2.00e-02 2.50e+03   1.53e-02 5.84e+00
        pdb=" CG  TRP B 632 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 632 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 632 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 632 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 632 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 632 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 632 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 632 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 632 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 911 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO B 912 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 912 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 912 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 911 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO A 912 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 912 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 912 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2631 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 571
        2.71 -     3.26: 14960
        3.26 -     3.80: 23866
        3.80 -     4.35: 28826
        4.35 -     4.90: 47822
  Nonbonded interactions: 116045
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" O   TYR B  67 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" O   TYR A  67 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   PRO B 716 "
            pdb=" OH  TYR D  27 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   PRO A 716 "
            pdb=" OH  TYR F  27 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OG  SER A 890 "
            pdb=" OH  TYR A 894 "
     model   vdw
     2.198 3.040
  ... (remaining 116040 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.230
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
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      :  0.005   0.341  15096  Z= 0.389
  Angle     :  0.609  12.171  20466  Z= 0.308
  Chirality :  0.042   0.153   2216
  Planarity :  0.003   0.043   2634
  Dihedral  : 17.057  88.702   5570
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.79 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.12 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.32 (0.20), residues: 1782
  helix:  0.44 (0.38), residues: 192
  sheet: -0.35 (0.28), residues: 352
  loop : -1.32 (0.18), residues: 1238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 882 
 TYR   0.015   0.001   TYR B 374 
 PHE   0.017   0.001   PHE A 572 
 TRP   0.041   0.002   TRP B 632 
 HIS   0.008   0.000   HIS A 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15048)
  covalent geometry    : angle       0.60738 (20374)
  SS BOND              : bond        0.00246 (   46)
  SS BOND              : angle       0.88504 (   92)
  hydrogen bonds       : bond        0.24102 (  314)
  hydrogen bonds       : angle       9.18251 (  861)
  Misc. bond           : bond        0.31750 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  843 MET cc_start: 0.8595 (tpp) cc_final: 0.7577 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1273
  time to fit residues: 12.0138
Evaluate side-chains
  47 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.082292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.051804 restraints weight = 62982.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.053486 restraints weight = 34208.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.054529 restraints weight = 24309.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.055164 restraints weight = 20033.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.055426 restraints weight = 17934.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15096  Z= 0.162
  Angle     :  0.613   9.527  20466  Z= 0.313
  Chirality :  0.044   0.143   2216
  Planarity :  0.005   0.129   2634
  Dihedral  :  4.396  19.126   1996
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.73 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 26.69 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.43 (0.20), residues: 1782
  helix: -0.05 (0.35), residues: 200
  sheet: -0.57 (0.27), residues: 364
  loop : -1.28 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG D  37 
 TYR   0.014   0.001   TYR A 374 
 PHE   0.016   0.001   PHE B 705 
 TRP   0.020   0.001   TRP B 632 
 HIS   0.005   0.001   HIS A 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (15048)
  covalent geometry    : angle       0.61138 (20374)
  SS BOND              : bond        0.00248 (   46)
  SS BOND              : angle       0.91374 (   92)
  hydrogen bonds       : bond        0.04934 (  314)
  hydrogen bonds       : angle       7.05018 (  861)
  Misc. bond           : bond        0.00695 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 55
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9040 (tp)
REVERT: A  843 MET cc_start: 0.8971 (tpp) cc_final: 0.7898 (mmm)
  outliers start: 31
  outliers final: 12
  residues processed: 82
  average time/residue: 0.1027
  time to fit residues: 13.1044
Evaluate side-chains
  63 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  373 SER
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   27 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 104 optimal weight:    0.2980
   chunk 107 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 165 optimal weight:    2.9990
   chunk 166 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.081398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.052096 restraints weight = 62297.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.053694 restraints weight = 33199.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.054721 restraints weight = 23127.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055330 restraints weight = 18724.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 76)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.055725 restraints weight = 16603.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  15096  Z= 0.168
  Angle     :  0.596   9.378  20466  Z= 0.305
  Chirality :  0.043   0.141   2216
  Planarity :  0.005   0.142   2634
  Dihedral  :  6.850 166.056   1996
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.90 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 26.63 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.49 (0.20), residues: 1782
  helix: -0.24 (0.35), residues: 200
  sheet: -0.59 (0.28), residues: 364
  loop : -1.30 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 882 
 TYR   0.017   0.001   TYR B 708 
 PHE   0.014   0.001   PHE A 705 
 TRP   0.028   0.001   TRP B 632 
 HIS   0.003   0.000   HIS A 440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (15048)
  covalent geometry    : angle       0.59502 (20374)
  SS BOND              : bond        0.00215 (   46)
  SS BOND              : angle       0.85241 (   92)
  hydrogen bonds       : bond        0.04682 (  314)
  hydrogen bonds       : angle       6.56423 (  861)
  Misc. bond           : bond        0.00863 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 59
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.5798 (m-90)
REVERT: A  442 MET cc_start: 0.8820 (tpp) cc_final: 0.8339 (tpp)
REVERT: A  472 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9067 (tp)
REVERT: A  843 MET cc_start: 0.8911 (tpp) cc_final: 0.7754 (mmm)
REVERT: B  412 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.5790 (m-90)
REVERT: B  567 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8771 (ptmt)
REVERT: B  843 MET cc_start: 0.9205 (tpp) cc_final: 0.8977 (tpp)
REVERT: F   53 LEU cc_start: 0.9184 (tp) cc_final: 0.8958 (tt)
  outliers start: 47
  outliers final: 25
  residues processed: 102
  average time/residue: 0.1126
  time to fit residues: 17.7580
Evaluate side-chains
  78 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 49
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  373 SER
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  567 LYS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   50 SER
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 73 optimal weight:   50.0000
   chunk 141 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 157 optimal weight:   10.0000
   chunk 161 optimal weight:   40.0000
   chunk 81 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
A 513 GLN
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 513 GLN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.079057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.048314 restraints weight = 64415.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.049819 restraints weight = 35519.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.050787 restraints weight = 25462.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.051368 restraints weight = 21005.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.051679 restraints weight = 18773.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.072  15096  Z= 0.369
  Angle     :  0.757   9.566  20466  Z= 0.380
  Chirality :  0.047   0.189   2216
  Planarity :  0.005   0.142   2634
  Dihedral  :  4.908  17.786   1996
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.32 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 24.15 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.73 (0.20), residues: 1782
  helix: -0.32 (0.34), residues: 200
  sheet: -0.82 (0.28), residues: 368
  loop : -1.47 (0.18), residues: 1214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.039   0.001   ARG D  37 
 TYR   0.048   0.002   TYR B 708 
 PHE   0.029   0.002   PHE B 482 
 TRP   0.015   0.002   TRP B 632 
 HIS   0.006   0.001   HIS B 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00843 (15048)
  covalent geometry    : angle       0.75395 (20374)
  SS BOND              : bond        0.00377 (   46)
  SS BOND              : angle       1.28187 (   92)
  hydrogen bonds       : bond        0.05013 (  314)
  hydrogen bonds       : angle       6.54271 (  861)
  Misc. bond           : bond        0.00582 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 54
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9141 (p)
REVERT: A  370 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8974 (mp)
REVERT: A  412 TRP cc_start: 0.8836 (OUTLIER) cc_final: 0.5853 (m-10)
REVERT: A  442 MET cc_start: 0.8994 (tpp) cc_final: 0.8454 (tpp)
REVERT: A  477 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8598 (p90)
REVERT: A  482 PHE cc_start: 0.7754 (t80) cc_final: 0.7432 (t80)
REVERT: A  635 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8537 (mp-120)
REVERT: A  843 MET cc_start: 0.8965 (tpp) cc_final: 0.7883 (mmm)
REVERT: B  223 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9156 (p)
REVERT: B  370 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8965 (mp)
REVERT: B  412 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.5849 (m-10)
REVERT: B  477 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8497 (p90)
REVERT: B  482 PHE cc_start: 0.7802 (t80) cc_final: 0.7389 (t80)
REVERT: B  635 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8482 (mp-120)
REVERT: F   53 LEU cc_start: 0.9249 (tp) cc_final: 0.9024 (tt)
  outliers start: 98
  outliers final: 45
  residues processed: 148
  average time/residue: 0.0816
  time to fit residues: 19.3882
Evaluate side-chains
  106 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 51
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  373 SER
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  582 LYS
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  831 THR
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   50 SER
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 160 optimal weight:   30.0000
   chunk 67 optimal weight:    0.6980
   chunk 154 optimal weight:   40.0000
   chunk 157 optimal weight:    8.9990
   chunk 129 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 121 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 177 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
A 589 GLN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 HIS
B 589 GLN
** B 845 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 = 0.3897 r_free = 0.3897 target = 0.080918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.051237 restraints weight = 62026.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.052841 restraints weight = 32710.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.053880 restraints weight = 22801.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.054475 restraints weight = 18481.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.054881 restraints weight = 16380.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  15096  Z= 0.137
  Angle     :  0.595  10.322  20466  Z= 0.306
  Chirality :  0.044   0.180   2216
  Planarity :  0.005   0.155   2634
  Dihedral  :  5.847 162.190   1996
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.57 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.57 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.58 (0.20), residues: 1782
  helix: -0.17 (0.34), residues: 200
  sheet: -0.84 (0.27), residues: 368
  loop : -1.33 (0.18), residues: 1214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG D  37 
 TYR   0.024   0.001   TYR B 708 
 PHE   0.019   0.001   PHE B 705 
 TRP   0.030   0.001   TRP B 632 
 HIS   0.005   0.001   HIS A 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (15048)
  covalent geometry    : angle       0.59333 (20374)
  SS BOND              : bond        0.00219 (   46)
  SS BOND              : angle       0.91343 (   92)
  hydrogen bonds       : bond        0.04212 (  314)
  hydrogen bonds       : angle       6.25171 (  861)
  Misc. bond           : bond        0.00657 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 55
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 SER cc_start: 0.9463 (OUTLIER) cc_final: 0.8899 (p)
REVERT: A  412 TRP cc_start: 0.8808 (OUTLIER) cc_final: 0.6009 (m-90)
REVERT: A  442 MET cc_start: 0.8957 (tpp) cc_final: 0.8423 (tpp)
REVERT: A  635 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (mp-120)
REVERT: A  843 MET cc_start: 0.8976 (tpp) cc_final: 0.7819 (mmm)
REVERT: B  186 SER cc_start: 0.9470 (OUTLIER) cc_final: 0.8895 (p)
REVERT: B  410 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8682 (pp30)
REVERT: B  412 TRP cc_start: 0.8803 (OUTLIER) cc_final: 0.5820 (m-10)
REVERT: B  482 PHE cc_start: 0.7433 (t80) cc_final: 0.7161 (t80)
REVERT: B  632 TRP cc_start: 0.6762 (p90) cc_final: 0.6535 (p90)
REVERT: B  635 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8103 (mp-120)
REVERT: F   53 LEU cc_start: 0.9134 (tp) cc_final: 0.8861 (tt)
  outliers start: 53
  outliers final: 36
  residues processed: 106
  average time/residue: 0.0890
  time to fit residues: 15.5053
Evaluate side-chains
  91 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 48
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  582 LYS
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 117 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 2 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 172 optimal weight:    0.0070
   chunk 85 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.081282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.051676 restraints weight = 61960.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.053313 restraints weight = 32494.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.054358 restraints weight = 22539.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.054985 restraints weight = 18246.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.055328 restraints weight = 16143.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15096  Z= 0.109
  Angle     :  0.572   9.718  20466  Z= 0.288
  Chirality :  0.043   0.202   2216
  Planarity :  0.004   0.068   2634
  Dihedral  :  4.373  18.106   1996
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.29 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 27.48 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.45 (0.20), residues: 1782
  helix: -0.06 (0.35), residues: 200
  sheet: -0.63 (0.28), residues: 348
  loop : -1.28 (0.18), residues: 1234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  37 
 TYR   0.018   0.001   TYR B 708 
 PHE   0.019   0.001   PHE C  28 
 TRP   0.021   0.001   TRP B 632 
 HIS   0.003   0.000   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (15048)
  covalent geometry    : angle       0.57098 (20374)
  SS BOND              : bond        0.00194 (   46)
  SS BOND              : angle       0.78103 (   92)
  hydrogen bonds       : bond        0.03829 (  314)
  hydrogen bonds       : angle       6.03942 (  861)
  Misc. bond           : bond        0.00509 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 51
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.5969 (m-90)
REVERT: A  582 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8176 (mttp)
REVERT: A  635 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (mp-120)
REVERT: A  698 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8693 (mm-30)
REVERT: A  843 MET cc_start: 0.8953 (tpp) cc_final: 0.7600 (mmm)
REVERT: B  410 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8635 (pp30)
REVERT: B  412 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.5878 (m-10)
REVERT: B  635 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8190 (mp-120)
REVERT: D   45 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6978 (mp0)
REVERT: F   53 LEU cc_start: 0.9125 (tp) cc_final: 0.8836 (tt)
  outliers start: 52
  outliers final: 30
  residues processed: 101
  average time/residue: 0.0906
  time to fit residues: 14.5029
Evaluate side-chains
  85 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 47
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  582 LYS
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 174 optimal weight:    4.9990
   chunk 102 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 124 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 178 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.081287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.051093 restraints weight = 63381.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.052753 restraints weight = 33814.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.053820 restraints weight = 23719.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.054457 restraints weight = 19303.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 67)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.054859 restraints weight = 17119.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15096  Z= 0.120
  Angle     :  0.569   9.257  20466  Z= 0.287
  Chirality :  0.043   0.192   2216
  Planarity :  0.005   0.201   2634
  Dihedral  :  5.579 156.497   1996
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.62 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 27.18 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.43 (0.20), residues: 1782
  helix: -0.04 (0.35), residues: 200
  sheet: -0.59 (0.29), residues: 332
  loop : -1.27 (0.18), residues: 1250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG F  37 
 TYR   0.017   0.001   TYR B 708 
 PHE   0.015   0.001   PHE B 705 
 TRP   0.035   0.001   TRP B 632 
 HIS   0.002   0.000   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (15048)
  covalent geometry    : angle       0.56810 (20374)
  SS BOND              : bond        0.00184 (   46)
  SS BOND              : angle       0.79257 (   92)
  hydrogen bonds       : bond        0.03768 (  314)
  hydrogen bonds       : angle       5.94541 (  861)
  Misc. bond           : bond        0.00316 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 53
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.6055 (m-90)
REVERT: A  442 MET cc_start: 0.8975 (tpp) cc_final: 0.8387 (tpp)
REVERT: A  582 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8188 (mttp)
REVERT: A  635 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8426 (mp-120)
REVERT: A  843 MET cc_start: 0.8827 (tpp) cc_final: 0.7696 (mmm)
REVERT: B  410 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8628 (pp30)
REVERT: B  412 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.5858 (m-10)
REVERT: B  635 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (mp-120)
REVERT: D   45 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7071 (mp0)
REVERT: F   38 ARG cc_start: 0.7955 (ptm-80) cc_final: 0.7073 (mpt180)
REVERT: F   53 LEU cc_start: 0.9112 (tp) cc_final: 0.8834 (tt)
  outliers start: 62
  outliers final: 40
  residues processed: 112
  average time/residue: 0.0982
  time to fit residues: 17.1170
Evaluate side-chains
  98 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 51
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  582 LYS
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  831 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 105 optimal weight:    0.1980
   chunk 137 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 131 optimal weight:    0.2980
   chunk 163 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 164 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 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 = 0.3912 r_free = 0.3912 target = 0.081584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.052090 restraints weight = 61986.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.053740 restraints weight = 32589.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.054747 restraints weight = 22568.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.055427 restraints weight = 18323.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.055854 restraints weight = 16145.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  15096  Z= 0.106
  Angle     :  0.573  10.118  20466  Z= 0.286
  Chirality :  0.043   0.187   2216
  Planarity :  0.003   0.044   2634
  Dihedral  :  4.270  18.091   1996
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.29 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 26.63 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.41 (0.20), residues: 1782
  helix:  0.08 (0.35), residues: 198
  sheet: -0.59 (0.29), residues: 332
  loop : -1.27 (0.18), residues: 1252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  37 
 TYR   0.017   0.001   TYR B 507 
 PHE   0.019   0.001   PHE E  28 
 TRP   0.028   0.001   TRP B 632 
 HIS   0.003   0.000   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (15048)
  covalent geometry    : angle       0.57218 (20374)
  SS BOND              : bond        0.00186 (   46)
  SS BOND              : angle       0.78369 (   92)
  hydrogen bonds       : bond        0.03665 (  314)
  hydrogen bonds       : angle       5.81629 (  861)
  Misc. bond           : bond        0.00250 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 52
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  223 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9110 (p)
REVERT: A  412 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.6159 (m-90)
REVERT: A  442 MET cc_start: 0.8926 (tpp) cc_final: 0.8331 (tpp)
REVERT: A  582 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8158 (mttp)
REVERT: A  635 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8271 (mp-120)
REVERT: A  843 MET cc_start: 0.8799 (tpp) cc_final: 0.7609 (mmm)
REVERT: B  410 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8528 (pp30)
REVERT: B  412 TRP cc_start: 0.8741 (OUTLIER) cc_final: 0.5705 (m-10)
REVERT: B  553 MET cc_start: 0.8032 (mtp) cc_final: 0.7774 (mtt)
REVERT: B  635 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8072 (mp-120)
REVERT: D   45 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7056 (mp0)
REVERT: F   53 LEU cc_start: 0.9064 (tp) cc_final: 0.8778 (tt)
  outliers start: 63
  outliers final: 40
  residues processed: 113
  average time/residue: 0.0848
  time to fit residues: 15.5569
Evaluate side-chains
  95 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 47
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  582 LYS
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  831 THR
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 161 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 126 optimal weight:    0.0010
   chunk 150 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.3392

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

Flipped N/Q/H residues before XYZ refinement:
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.081072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.050902 restraints weight = 64064.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.052558 restraints weight = 34292.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.053628 restraints weight = 24050.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.054272 restraints weight = 19514.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.054620 restraints weight = 17276.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  15096  Z= 0.162
  Angle     :  0.604  10.484  20466  Z= 0.302
  Chirality :  0.044   0.281   2216
  Planarity :  0.005   0.144   2634
  Dihedral  :  4.369  20.890   1996
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.73 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 26.94 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.43 (0.20), residues: 1782
  helix:  0.11 (0.36), residues: 198
  sheet: -0.58 (0.29), residues: 332
  loop : -1.29 (0.18), residues: 1252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG F  37 
 TYR   0.067   0.002   TYR A 708 
 PHE   0.015   0.001   PHE A 705 
 TRP   0.043   0.001   TRP B 632 
 HIS   0.003   0.001   HIS A 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (15048)
  covalent geometry    : angle       0.60251 (20374)
  SS BOND              : bond        0.00218 (   46)
  SS BOND              : angle       0.88075 (   92)
  hydrogen bonds       : bond        0.03895 (  314)
  hydrogen bonds       : angle       5.89150 (  861)
  Misc. bond           : bond        0.01122 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 51
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8674 (pm20)
REVERT: A  223 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9130 (p)
REVERT: A  412 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.6147 (m-90)
REVERT: A  442 MET cc_start: 0.8956 (tpp) cc_final: 0.8355 (tpp)
REVERT: A  635 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8351 (mp-120)
REVERT: A  843 MET cc_start: 0.8816 (tpp) cc_final: 0.7655 (mmm)
REVERT: B  103 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8679 (pm20)
REVERT: B  410 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8626 (pp30)
REVERT: B  412 TRP cc_start: 0.8755 (OUTLIER) cc_final: 0.5797 (m-10)
REVERT: B  553 MET cc_start: 0.8091 (mtp) cc_final: 0.7831 (mtt)
REVERT: B  635 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8192 (mp-120)
REVERT: D   45 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7101 (mp0)
REVERT: F   53 LEU cc_start: 0.9094 (tp) cc_final: 0.8802 (tt)
  outliers start: 64
  outliers final: 45
  residues processed: 113
  average time/residue: 0.0878
  time to fit residues: 16.8634
Evaluate side-chains
  102 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 48
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  831 THR
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 177 optimal weight:    1.9990
   chunk 172 optimal weight:    0.1980
   chunk 61 optimal weight:    6.9990
   chunk 153 optimal weight:    8.9990
   chunk 136 optimal weight:    0.0870
   chunk 43 optimal weight:    0.8980
   chunk 154 optimal weight:   20.0000
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 148 optimal weight:   10.0000
   chunk 143 optimal weight:    7.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.081423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.051961 restraints weight = 62236.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.053593 restraints weight = 32892.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.054642 restraints weight = 22887.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.055275 restraints weight = 18510.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.055667 restraints weight = 16340.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15096  Z= 0.122
  Angle     :  0.597  10.712  20466  Z= 0.299
  Chirality :  0.044   0.395   2216
  Planarity :  0.004   0.113   2634
  Dihedral  :  4.337  28.429   1996
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.51 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 27.06 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.43 (0.20), residues: 1782
  helix:  0.08 (0.36), residues: 198
  sheet: -0.58 (0.29), residues: 332
  loop : -1.29 (0.18), residues: 1252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG F  37 
 TYR   0.062   0.001   TYR A 708 
 PHE   0.019   0.001   PHE E  28 
 TRP   0.040   0.001   TRP B 632 
 HIS   0.003   0.000   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (15048)
  covalent geometry    : angle       0.59592 (20374)
  SS BOND              : bond        0.00280 (   46)
  SS BOND              : angle       0.84793 (   92)
  hydrogen bonds       : bond        0.03895 (  314)
  hydrogen bonds       : angle       5.90805 (  861)
  Misc. bond           : bond        0.00839 (    2)

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

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

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3564 Ramachandran restraints generated.
    1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 51
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8675 (pm20)
REVERT: A  223 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9142 (p)
REVERT: A  412 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.6081 (m-10)
REVERT: A  442 MET cc_start: 0.8922 (tpp) cc_final: 0.8317 (tpp)
REVERT: A  553 MET cc_start: 0.7862 (mtp) cc_final: 0.7619 (mtt)
REVERT: A  635 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8307 (mp-120)
REVERT: A  843 MET cc_start: 0.8821 (tpp) cc_final: 0.7688 (mmm)
REVERT: B  103 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8674 (pm20)
REVERT: B  410 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8535 (pp30)
REVERT: B  412 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.5694 (m-90)
REVERT: B  442 MET cc_start: 0.9298 (mmm) cc_final: 0.8840 (mmm)
REVERT: B  553 MET cc_start: 0.8051 (mtp) cc_final: 0.7816 (mtp)
REVERT: B  635 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8164 (mp-120)
REVERT: D   45 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7091 (mp0)
REVERT: F   53 LEU cc_start: 0.9042 (tp) cc_final: 0.8733 (tt)
  outliers start: 58
  outliers final: 45
  residues processed: 107
  average time/residue: 0.0830
  time to fit residues: 15.1002
Evaluate side-chains
  103 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 49
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  212 CYS
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  802 THR
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 THR
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  212 CYS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  586 ILE
Chi-restraints excluded: chain B residue  635 GLN
Chi-restraints excluded: chain B residue  718 LYS
Chi-restraints excluded: chain B residue  795 LEU
Chi-restraints excluded: chain B residue  802 THR
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain B residue  831 THR
Chi-restraints excluded: chain B residue  853 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   27 TYR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   13 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   42 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 157 optimal weight:    8.9990
   chunk 32 optimal weight:    0.1980
   chunk 174 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 129 optimal weight:    0.6980
   chunk 100 optimal weight:    8.9990
   chunk 159 optimal weight:   40.0000
   chunk 58 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 ASN
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  18 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 = 0.3923 r_free = 0.3923 target = 0.082018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.052191 restraints weight = 63377.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.053900 restraints weight = 33669.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.054999 restraints weight = 23486.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.055658 restraints weight = 19026.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.056090 restraints weight = 16831.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  15096  Z= 0.105
  Angle     :  0.587  10.488  20466  Z= 0.293
  Chirality :  0.044   0.294   2216
  Planarity :  0.004   0.060   2634
  Dihedral  :  4.235  27.148   1996
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.29 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 27.24 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 aren not related in a simple way.
  whole: -1.39 (0.20), residues: 1782
  helix:  0.07 (0.36), residues: 200
  sheet: -0.51 (0.29), residues: 332
  loop : -1.27 (0.18), residues: 1250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  37 
 TYR   0.050   0.001   TYR A 708 
 PHE   0.017   0.001   PHE A 705 
 TRP   0.038   0.001   TRP B 632 
 HIS   0.004   0.000   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (15048)
  covalent geometry    : angle       0.58560 (20374)
  SS BOND              : bond        0.00174 (   46)
  SS BOND              : angle       0.78659 (   92)
  hydrogen bonds       : bond        0.03928 (  314)
  hydrogen bonds       : angle       5.83800 (  861)
  Misc. bond           : bond        0.00776 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3081.60 seconds
wall clock time: 53 minutes 29.57 seconds (3209.57 seconds total)