Starting phenix.real_space_refine
on Thu Jul 31 08:54:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8de6_27385/07_2025/8de6_27385.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.144
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S     101      5.16       5
     C    8256      2.51       5
     N    2271      2.21       5
     O    2612      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13243
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "E"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 929
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "F"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 834
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3202
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 15, 'TRANS': 385}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 929
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "I"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 834
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "C"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3202
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 15, 'TRANS': 385}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3202
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 15, 'TRANS': 385}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 37
          Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 37
          Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 37
          Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 7.43, per 1000 atoms: 0.56
  Number of scatterers: 13243
  At special positions: 0
  Unit cell: (149.8, 119, 105, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S     101     16.00
     O    2612      8.00
     N    2271      7.00
     C    8256      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=34, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  42 " - pdb=" SG  CYS F 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  57 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  67 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  73 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A  91 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  86 " - pdb=" SG  CYS A 104 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 113 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 460 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 447 " - pdb=" SG  CYS A 462 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 464 " - pdb=" SG  CYS A 473 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 114 " distance=2.05
    Simple disulfide: pdb=" SG  CYS I  42 " - pdb=" SG  CYS I 107 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  57 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C  91 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  86 " - pdb=" SG  CYS C 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  98 " - pdb=" SG  CYS C 113 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 121 " - pdb=" SG  CYS C 160 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 444 " - pdb=" SG  CYS C 460 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 447 " - pdb=" SG  CYS C 462 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 464 " - pdb=" SG  CYS C 473 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  57 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  33 " - pdb=" SG  CYS G  67 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  36 " - pdb=" SG  CYS G  73 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  80 " - pdb=" SG  CYS G  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  86 " - pdb=" SG  CYS G 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  98 " - pdb=" SG  CYS G 113 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 121 " - pdb=" SG  CYS G 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 444 " - pdb=" SG  CYS G 460 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 447 " - pdb=" SG  CYS G 462 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 464 " - pdb=" SG  CYS G 473 " 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
      
  Atom "HETATM13167  O5  BMA A 603 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=6, symmetry=0
  Links applied
    NAG-THR
      " NAG A 601 " - " THR A 452 "
      " NAG C 601 " - " THR C 452 "
      " NAG G 601 " - " THR G 452 "
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3060

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 28 sheets defined
      18.2% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'E' and resid 47 through 51
      removed outlier: 3.586A  pdb=" N   VAL E  50 " --> pdb=" O   SER E  47 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR E  51 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 47 through 51'
    Processing helix  chain 'E' and resid 105 through 109
      removed outlier: 3.693A  pdb=" N   ASP E 108 " --> pdb=" O   GLN E 105 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   THR E 109 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 105 through 109'
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 109 through 113
      removed outlier: 3.834A  pdb=" N   ASP A 112 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   CYS A 113 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 109 through 113'
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 279 through 291
    Processing helix  chain 'A' and resid 369 through 381
      removed outlier: 3.614A  pdb=" N   GLU A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLY A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 396
      removed outlier: 4.450A  pdb=" N   PHE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 411 through 414
      removed outlier: 3.523A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 411 through 414'
    Processing helix  chain 'A' and resid 420 through 438
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.596A  pdb=" N   LYS A 443 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.899A  pdb=" N   VAL B  50 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 83
      removed outlier: 3.695A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 80 through 83'
    Processing helix  chain 'I' and resid 98 through 102
      removed outlier: 3.721A  pdb=" N   VAL I 102 " --> pdb=" O   GLN I  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 97
    Processing helix  chain 'C' and resid 109 through 113
      removed outlier: 4.045A  pdb=" N   ASP C 112 " --> pdb=" O   ASP C 109 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   CYS C 113 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 109 through 113'
    Processing helix  chain 'C' and resid 129 through 134
      removed outlier: 4.086A  pdb=" N   THR C 134 " --> pdb=" O   GLU C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 273
    Processing helix  chain 'C' and resid 279 through 291
    Processing helix  chain 'C' and resid 369 through 381
      removed outlier: 3.516A  pdb=" N   LEU C 379 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG C 380 " --> pdb=" O   GLU C 376 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY C 381 " --> pdb=" O   LYS C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 396
      removed outlier: 4.438A  pdb=" N   PHE C 389 " --> pdb=" O   ASP C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 399
      No H-bonds generated for 'chain 'C' and resid 397 through 399'
    Processing helix  chain 'C' and resid 411 through 414
    Processing helix  chain 'C' and resid 420 through 438
    Processing helix  chain 'C' and resid 440 through 444
      removed outlier: 3.546A  pdb=" N   LYS C 443 " --> pdb=" O   SER C 440 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 97
    Processing helix  chain 'G' and resid 109 through 113
      removed outlier: 4.091A  pdb=" N   ASP G 112 " --> pdb=" O   ASP G 109 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   CYS G 113 " --> pdb=" O   GLU G 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 109 through 113'
    Processing helix  chain 'G' and resid 130 through 134
      removed outlier: 3.949A  pdb=" N   THR G 134 " --> pdb=" O   LEU G 131 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 264 through 273
    Processing helix  chain 'G' and resid 279 through 291
    Processing helix  chain 'G' and resid 369 through 381
      removed outlier: 3.834A  pdb=" N   ARG G 380 " --> pdb=" O   GLU G 376 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY G 381 " --> pdb=" O   LYS G 377 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 385 through 396
      removed outlier: 4.500A  pdb=" N   PHE G 389 " --> pdb=" O   ASP G 385 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 397 through 399
      No H-bonds generated for 'chain 'G' and resid 397 through 399'
    Processing helix  chain 'G' and resid 411 through 414
    Processing helix  chain 'G' and resid 420 through 438
    Processing helix  chain 'G' and resid 440 through 444
    Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 26
    Processing sheet with id=AA2, first strand: chain 'E' and resid 30 through 31
      removed outlier: 3.809A  pdb=" N   VAL E  31 " --> pdb=" O   THR E 137 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   VAL E  53 " --> pdb=" O   MET E  69 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   MET E  69 " --> pdb=" O   VAL E  53 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TRP E  55 " --> pdb=" O   LEU E  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 29 through 32
      removed outlier: 6.415A  pdb=" N   LEU F  30 " --> pdb=" O   GLU F 124 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE F  67 " --> pdb=" O   TRP F  54 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   GLN F  56 " --> pdb=" O   LEU F  65 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   LEU F  65 " --> pdb=" O   GLN F  56 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   LYS F  58 " --> pdb=" O   LEU F  63 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   LEU F  63 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 38 through 43
      removed outlier: 3.705A  pdb=" N   ASP F  89 " --> pdb=" O   SER F  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 24
      removed outlier: 6.909A  pdb=" N   ARG A  23 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 43
    Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 128
      removed outlier: 6.689A  pdb=" N   GLU A 127 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A 170 " --> pdb=" O   ASP A 165 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AB1, first strand: chain 'A' and resid 178 through 199
      removed outlier: 6.002A  pdb=" N   VAL A 255 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LEU A 181 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ARG A 253 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   TYR A 183 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   LEU A 251 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
      removed outlier: 9.294A  pdb=" N   THR A 185 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   ILE A 249 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
      removed outlier: 9.343A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 9.131A  pdb=" N   GLY A 247 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 9.283A  pdb=" N   LYS A 189 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 8.982A  pdb=" N   VAL A 245 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 8.999A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   LEU A 243 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   THR A 193 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   MET A 241 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   HIS A 195 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   GLU A 239 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 8.931A  pdb=" N   GLU A 197 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
      removed outlier: 8.888A  pdb=" N   LYS A 237 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU A 239 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR A 308 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 247 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU A 300 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ARG A 253 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLY A 298 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET A 315 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 350 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 349 through 364
    current: chain 'C' and resid 234 through 256
      removed outlier: 3.882A  pdb=" N   LYS C 237 " --> pdb=" O   SER C 314 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY C 247 " --> pdb=" O   TYR C 304 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR C 304 " --> pdb=" O   GLY C 247 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LEU C 300 " --> pdb=" O   LEU C 251 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ARG C 253 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLY C 298 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU C 362 " --> pdb=" O   GLU C 305 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   MET C 315 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER C 352 " --> pdb=" O   MET C 315 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 351 through 364
    current: chain 'G' and resid 237 through 256
      removed outlier: 3.788A  pdb=" N   TYR G 308 " --> pdb=" O   LEU G 243 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY G 247 " --> pdb=" O   TYR G 304 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU G 300 " --> pdb=" O   LEU G 251 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ARG G 253 " --> pdb=" O   GLY G 298 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY G 298 " --> pdb=" O   ARG G 253 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU G 303 " --> pdb=" O   ARG G 364 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET G 315 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER G 352 " --> pdb=" O   MET G 315 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 455
    Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 24
      removed outlier: 3.649A  pdb=" N   GLN B  96 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 31
      removed outlier: 3.695A  pdb=" N   VAL B  31 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA B 110 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL B  53 " --> pdb=" O   MET B  69 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   MET B  69 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   TRP B  55 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 32
      removed outlier: 6.271A  pdb=" N   LEU I  30 " --> pdb=" O   GLU I 124 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 38 through 43
      removed outlier: 3.656A  pdb=" N   ASP I  89 " --> pdb=" O   SER I  86 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 72 through 73
      removed outlier: 3.752A  pdb=" N   THR I  62 " --> pdb=" O   LYS I  58 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS I  58 " --> pdb=" O   THR I  62 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS I  64 " --> pdb=" O   GLN I  56 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP I  54 " --> pdb=" O   LEU I  66 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   TYR I  68 " --> pdb=" O   LEU I  52 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU I  52 " --> pdb=" O   TYR I  68 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 24
      removed outlier: 6.898A  pdb=" N   ARG C  23 " --> pdb=" O   GLU C  47 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 43
      removed outlier: 3.554A  pdb=" N   ARG C  42 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 51
      removed outlier: 6.665A  pdb=" N   GLY C  50 " --> pdb=" O   CYS C 460 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   CYS C 462 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85
    Processing sheet with id=AC3, first strand: chain 'C' and resid 127 through 128
      removed outlier: 6.813A  pdb=" N   GLU C 127 " --> pdb=" O   ARG C 173 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR C 170 " --> pdb=" O   ASP C 165 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 138 through 139
    Processing sheet with id=AC5, first strand: chain 'G' and resid 23 through 24
      removed outlier: 6.862A  pdb=" N   ARG G  23 " --> pdb=" O   GLU G  47 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 43
    Processing sheet with id=AC7, first strand: chain 'G' and resid 84 through 85
    Processing sheet with id=AC8, first strand: chain 'G' and resid 127 through 128
      removed outlier: 6.618A  pdb=" N   GLU G 127 " --> pdb=" O   ARG G 173 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR G 170 " --> pdb=" O   ASP G 165 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 138 through 139
    Processing sheet with id=AD1, first strand: chain 'G' and resid 452 through 455

    372 hydrogen bonds defined for protein.
    984 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: 4.22

  Time building geometry restraints manager: 3.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3630
        1.33 -     1.46: 3616
        1.46 -     1.59: 6121
        1.59 -     1.72: 0
        1.72 -     1.85: 134
  Bond restraints: 13501
  Sorted by residual:
  bond pdb=" C2  BMA C 602 "
       pdb=" O2  BMA C 602 "
    ideal  model  delta    sigma   weight residual
    1.402  1.461 -0.059 2.00e-02 2.50e+03 8.72e+00
  bond pdb=" C1  BMA G 603 "
       pdb=" C2  BMA G 603 "
    ideal  model  delta    sigma   weight residual
    1.519  1.569 -0.050 2.00e-02 2.50e+03 6.22e+00
  bond pdb=" C   ALA G 399 "
       pdb=" N   PRO G 400 "
    ideal  model  delta    sigma   weight residual
    1.328  1.298  0.030 1.25e-02 6.40e+03 5.61e+00
  bond pdb=" C2  BMA C 602 "
       pdb=" C3  BMA C 602 "
    ideal  model  delta    sigma   weight residual
    1.544  1.501  0.043 2.00e-02 2.50e+03 4.72e+00
  bond pdb=" CA  ASP B  91 "
       pdb=" CB  ASP B  91 "
    ideal  model  delta    sigma   weight residual
    1.522  1.494  0.027 1.27e-02 6.20e+03 4.66e+00
  ... (remaining 13496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 16764
        1.58 -     3.15: 1312
        3.15 -     4.73: 115
        4.73 -     6.31: 26
        6.31 -     7.89: 8
  Bond angle restraints: 18225
  Sorted by residual:
  angle pdb=" C   ARG C 122 "
        pdb=" N   ASP C 123 "
        pdb=" CA  ASP C 123 "
      ideal   model   delta    sigma   weight residual
     121.54  127.22   -5.68 1.91e+00 2.74e-01 8.85e+00
  angle pdb=" N   THR I  26 "
        pdb=" CA  THR I  26 "
        pdb=" C   THR I  26 "
      ideal   model   delta    sigma   weight residual
     110.97  114.14   -3.17 1.09e+00 8.42e-01 8.48e+00
  angle pdb=" N   LEU G 407 "
        pdb=" CA  LEU G 407 "
        pdb=" C   LEU G 407 "
      ideal   model   delta    sigma   weight residual
     110.28  114.47   -4.19 1.48e+00 4.57e-01 8.01e+00
  angle pdb=" C4  BMA A 603 "
        pdb=" C5  BMA A 603 "
        pdb=" O5  BMA A 603 "
      ideal   model   delta    sigma   weight residual
     113.24  105.35    7.89 3.00e+00 1.11e-01 6.91e+00
  angle pdb=" C1  BMA C 602 "
        pdb=" O5  BMA C 602 "
        pdb=" C5  BMA C 602 "
      ideal   model   delta    sigma   weight residual
     118.82  111.11    7.71 3.00e+00 1.11e-01 6.60e+00
  ... (remaining 18220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 7966
       22.75 -    45.51: 271
       45.51 -    68.26: 31
       68.26 -    91.01: 37
       91.01 -   113.76: 24
  Dihedral angle restraints: 8329
    sinusoidal: 3547
      harmonic: 4782
  Sorted by residual:
  dihedral pdb=" O4  BMA A 602 "
           pdb=" C4  BMA A 602 "
           pdb=" C5  BMA A 602 "
           pdb=" O5  BMA A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  174.95  113.76     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" O4  BMA A 603 "
           pdb=" C4  BMA A 603 "
           pdb=" C5  BMA A 603 "
           pdb=" O5  BMA A 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  175.65  113.06     1      3.00e+01 1.11e-03 1.48e+01
  dihedral pdb=" O4  BMA G 603 "
           pdb=" C4  BMA G 603 "
           pdb=" C5  BMA G 603 "
           pdb=" O5  BMA G 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  177.12  111.59     1      3.00e+01 1.11e-03 1.46e+01
  ... (remaining 8326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1498
       0.067 -    0.135: 420
       0.135 -    0.202: 55
       0.202 -    0.270: 1
       0.270 -    0.337: 6
  Chirality restraints: 1980
  Sorted by residual:
  chirality pdb=" C5  BMA C 602 "
            pdb=" C4  BMA C 602 "
            pdb=" C6  BMA C 602 "
            pdb=" O5  BMA C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.61    0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" C2  BMA C 603 "
            pdb=" C1  BMA C 603 "
            pdb=" C3  BMA C 603 "
            pdb=" O2  BMA C 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.80   -0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" C5  BMA C 603 "
            pdb=" C4  BMA C 603 "
            pdb=" C6  BMA C 603 "
            pdb=" O5  BMA C 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.60    0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 1977 not shown)

  Planarity restraints: 2359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  58 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO F  59 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO F  59 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO F  59 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP G 260 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   ASP G 260 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASP G 260 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL G 261 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F  54 "   -0.001 2.00e-02 2.50e+03   1.31e-02 4.30e+00
        pdb=" CG  TRP F  54 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TRP F  54 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP F  54 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP F  54 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP F  54 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP F  54 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F  54 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F  54 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP F  54 "    0.019 2.00e-02 2.50e+03
  ... (remaining 2356 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 556
        2.72 -     3.26: 12048
        3.26 -     3.81: 18695
        3.81 -     4.35: 23607
        4.35 -     4.90: 42554
  Nonbonded interactions: 97460
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP G 270 "
            pdb=" OH  TYR G 290 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OD2 ASP A 270 "
            pdb=" OH  TYR A 290 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD2 ASP G 109 "
            pdb="CA    CA G 604 "
     model   vdw
     2.203 2.510
  nonbonded pdb=" OG1 THR A 452 "
            pdb=" N2  NAG A 601 "
     model   vdw
     2.256 2.496
  nonbonded pdb=" OG1 THR G 452 "
            pdb=" N2  NAG G 601 "
     model   vdw
     2.268 2.496
  ... (remaining 97455 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'I'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.930
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.070
  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:3.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.010   0.071  13544  Z= 0.535
  Angle     :  0.931   7.885  18299  Z= 0.522
  Chirality :  0.061   0.337   1980
  Planarity :  0.007   0.058   2359
  Dihedral  : 14.683 113.764   5167
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  6.76 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.20), residues: 1633
  helix: -0.06 (0.30), residues: 219
  sheet: -0.28 (0.22), residues: 512
  loop : -0.83 (0.20), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.008   TRP C  30 
 HIS   0.018   0.005   HIS G 244 
 PHE   0.024   0.006   PHE A 389 
 TYR   0.026   0.006   TYR G 290 
 ARG   0.021   0.004   ARG G  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25970 (  372)
  hydrogen bonds       : angle       8.17558 (  984)
  SS BOND              : bond        0.01272 (   34)
  SS BOND              : angle       1.24028 (   68)
  link_NAG-THR         : bond        0.01170 (    3)
  link_NAG-THR         : angle       3.28575 (    6)
  covalent geometry    : bond        0.01021 (13501)
  covalent geometry    : angle       0.92818 (18225)
  Misc. bond           : bond        0.00416 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 312
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   22 GLN cc_start: 0.8830 (pt0) cc_final: 0.8275 (pt0)
REVERT: E   96 GLN cc_start: 0.9015 (mt0) cc_final: 0.8814 (mt0)
REVERT: E  100 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7666 (mmmm)
REVERT: F   43 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7051 (mtm110)
REVERT: A   56 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7455 (ptp-110)
REVERT: A   77 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7662 (pm20)
REVERT: A  234 TYR cc_start: 0.7316 (t80) cc_final: 0.7076 (t80)
REVERT: A  241 MET cc_start: 0.8640 (ttm) cc_final: 0.8380 (ttp)
REVERT: A  250 HIS cc_start: 0.8653 (m-70) cc_final: 0.7784 (t70)
REVERT: A  269 ASP cc_start: 0.8576 (m-30) cc_final: 0.8122 (m-30)
REVERT: A  406 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8317 (ttmm)
REVERT: A  433 GLU cc_start: 0.7711 (tt0) cc_final: 0.7130 (mt-10)
REVERT: A  456 MET cc_start: 0.8051 (mmm) cc_final: 0.7791 (mmm)
REVERT: B   62 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7156 (mmtm)
REVERT: B   91 ASP cc_start: 0.7310 (t0) cc_final: 0.6843 (t70)
REVERT: B  100 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6960 (mmtt)
REVERT: B  108 ASP cc_start: 0.7820 (m-30) cc_final: 0.7560 (m-30)
REVERT: I   23 MET cc_start: 0.8661 (mmm) cc_final: 0.8418 (mmm)
REVERT: I   82 SER cc_start: 0.7802 (m) cc_final: 0.7526 (p)
REVERT: I   96 ASN cc_start: 0.7923 (m110) cc_final: 0.7701 (m110)
REVERT: I  123 LEU cc_start: 0.7649 (tp) cc_final: 0.7427 (tt)
REVERT: C   23 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.8017 (ttp80)
REVERT: C  101 ASP cc_start: 0.7324 (m-30) cc_final: 0.7080 (m-30)
REVERT: C  107 PHE cc_start: 0.7059 (m-80) cc_final: 0.6851 (m-80)
REVERT: C  171 TYR cc_start: 0.8195 (m-80) cc_final: 0.7969 (m-80)
REVERT: C  182 ILE cc_start: 0.8512 (mt) cc_final: 0.8086 (mp)
REVERT: C  185 THR cc_start: 0.8177 (m) cc_final: 0.7917 (p)
REVERT: C  192 ARG cc_start: 0.6929 (ttm170) cc_final: 0.6351 (mmp80)
REVERT: C  240 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7668 (mmtp)
REVERT: C  251 LEU cc_start: 0.8401 (tp) cc_final: 0.8129 (tp)
REVERT: C  272 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7869 (mtpp)
REVERT: G   19 HIS cc_start: 0.6191 (p-80) cc_final: 0.5979 (p90)
REVERT: G   45 SER cc_start: 0.7802 (t) cc_final: 0.7524 (p)
REVERT: G   56 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6902 (ptm160)
REVERT: G   79 ASP cc_start: 0.7531 (m-30) cc_final: 0.7263 (p0)
REVERT: G  269 ASP cc_start: 0.8023 (m-30) cc_final: 0.7514 (m-30)
REVERT: G  270 ASP cc_start: 0.7994 (m-30) cc_final: 0.7711 (m-30)
REVERT: G  315 MET cc_start: 0.7638 (ttp) cc_final: 0.7357 (tmm)
REVERT: G  379 LEU cc_start: 0.8084 (tp) cc_final: 0.7741 (tp)
REVERT: G  406 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7949 (tmtt)
REVERT: G  459 LYS cc_start: 0.7790 (tttm) cc_final: 0.7378 (tttt)
  outliers start: 37
  outliers final: 20
  residues processed: 339
  average time/residue: 0.3501
  time to fit residues: 164.7853
Evaluate side-chains
  246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 225
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue  101 ASP
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue  125 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  453 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 138 optimal weight:    0.3980
   chunk 124 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 148 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E  96 GLN
F  25 GLN
A  32 GLN
A 153 ASN
A 177 ASN
A 199 GLN
A 258 ASN
B  20 GLN
C  39 GLN
C 177 ASN
C 293 HIS
C 354 ASN
C 448 GLN
C 449 ASN
G  85 GLN
G 157 ASN
G 177 ASN
G 449 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.146523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.113435 restraints weight = 16210.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.48
r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13544  Z= 0.114
  Angle     :  0.527   6.044  18299  Z= 0.274
  Chirality :  0.042   0.157   1980
  Planarity :  0.004   0.051   2359
  Dihedral  : 11.660  72.863   2038
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 10.38 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.20), residues: 1633
  helix:  0.74 (0.33), residues: 228
  sheet: -0.19 (0.22), residues: 572
  loop : -0.79 (0.21), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  66 
 HIS   0.002   0.001   HIS I  46 
 PHE   0.009   0.001   PHE C 439 
 TYR   0.012   0.001   TYR G 294 
 ARG   0.004   0.000   ARG A 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  372)
  hydrogen bonds       : angle       5.43785 (  984)
  SS BOND              : bond        0.00380 (   34)
  SS BOND              : angle       0.86296 (   68)
  link_NAG-THR         : bond        0.00154 (    3)
  link_NAG-THR         : angle       2.21498 (    6)
  covalent geometry    : bond        0.00251 (13501)
  covalent geometry    : angle       0.52354 (18225)
  Misc. bond           : bond        0.00096 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 231
  time to evaluate  : 1.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   96 GLN cc_start: 0.8957 (mt0) cc_final: 0.8748 (mt0)
REVERT: E  100 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7783 (mmmm)
REVERT: F   26 THR cc_start: 0.8535 (p) cc_final: 0.8102 (p)
REVERT: F   43 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7338 (ptp90)
REVERT: A   56 ARG cc_start: 0.7859 (ptp90) cc_final: 0.7508 (ptp-110)
REVERT: A   77 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7624 (pm20)
REVERT: A  192 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8206 (ttm110)
REVERT: A  234 TYR cc_start: 0.7497 (t80) cc_final: 0.7205 (t80)
REVERT: A  250 HIS cc_start: 0.8757 (m-70) cc_final: 0.7980 (t70)
REVERT: A  369 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8188 (tttp)
REVERT: A  406 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8320 (ttmm)
REVERT: A  433 GLU cc_start: 0.8230 (tt0) cc_final: 0.7666 (mt-10)
REVERT: A  456 MET cc_start: 0.8371 (mmm) cc_final: 0.8042 (mmm)
REVERT: B   82 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8546 (pp)
REVERT: B   91 ASP cc_start: 0.7174 (t0) cc_final: 0.6601 (t70)
REVERT: B  100 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7271 (mmmt)
REVERT: B  108 ASP cc_start: 0.7963 (m-30) cc_final: 0.7654 (m-30)
REVERT: B  132 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7778 (tp-100)
REVERT: I   23 MET cc_start: 0.8847 (mmm) cc_final: 0.8301 (mmm)
REVERT: C   24 MET cc_start: 0.9093 (mtp) cc_final: 0.8884 (mmm)
REVERT: C  101 ASP cc_start: 0.7447 (m-30) cc_final: 0.7214 (m-30)
REVERT: C  182 ILE cc_start: 0.8809 (mt) cc_final: 0.8507 (tt)
REVERT: C  192 ARG cc_start: 0.7675 (ttm170) cc_final: 0.6517 (mmp80)
REVERT: C  240 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8186 (mmtp)
REVERT: C  243 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (mm)
REVERT: C  272 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8143 (tttm)
REVERT: G   19 HIS cc_start: 0.6230 (p-80) cc_final: 0.6017 (p90)
REVERT: G   56 ARG cc_start: 0.7664 (ptp90) cc_final: 0.7337 (ptm160)
REVERT: G   85 GLN cc_start: 0.7818 (tp40) cc_final: 0.7531 (tp40)
REVERT: G  282 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: G  376 GLU cc_start: 0.7551 (tp30) cc_final: 0.6819 (tt0)
REVERT: G  453 VAL cc_start: 0.8020 (t) cc_final: 0.7629 (p)
  outliers start: 38
  outliers final: 20
  residues processed: 259
  average time/residue: 0.3810
  time to fit residues: 136.1321
Evaluate side-chains
  232 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  419 LYS
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue  125 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  396 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   chunk 124 optimal weight:    5.9990
   chunk 141 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 199 GLN
A 293 HIS
C 412 ASN
G 190 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107208 restraints weight = 16429.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.48
r_work: 0.3084 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13544  Z= 0.199
  Angle     :  0.584   6.961  18299  Z= 0.306
  Chirality :  0.045   0.158   1980
  Planarity :  0.004   0.052   2359
  Dihedral  :  8.616  59.888   2026
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 12.16 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.20), residues: 1633
  helix:  0.62 (0.33), residues: 225
  sheet: -0.14 (0.22), residues: 540
  loop : -1.07 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G  27 
 HIS   0.005   0.001   HIS I  46 
 PHE   0.015   0.002   PHE C 191 
 TYR   0.021   0.002   TYR G 137 
 ARG   0.007   0.001   ARG G  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05263 (  372)
  hydrogen bonds       : angle       4.96062 (  984)
  SS BOND              : bond        0.00417 (   34)
  SS BOND              : angle       1.01979 (   68)
  link_NAG-THR         : bond        0.00281 (    3)
  link_NAG-THR         : angle       2.42311 (    6)
  covalent geometry    : bond        0.00477 (13501)
  covalent geometry    : angle       0.58039 (18225)
  Misc. bond           : bond        0.00092 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 203
  time to evaluate  : 1.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7782 (mmmm)
REVERT: F   26 THR cc_start: 0.8705 (p) cc_final: 0.8179 (p)
REVERT: F   43 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7544 (mtt90)
REVERT: A   56 ARG cc_start: 0.8135 (ptp90) cc_final: 0.7910 (ptp-110)
REVERT: A   77 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7629 (pm20)
REVERT: A  149 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9221 (p)
REVERT: A  192 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8268 (ttm110)
REVERT: A  234 TYR cc_start: 0.7827 (t80) cc_final: 0.7577 (t80)
REVERT: A  241 MET cc_start: 0.8926 (ttp) cc_final: 0.8623 (ttp)
REVERT: A  250 HIS cc_start: 0.8769 (m-70) cc_final: 0.7954 (t70)
REVERT: A  260 ASP cc_start: 0.8733 (t0) cc_final: 0.8502 (t0)
REVERT: A  369 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8205 (tttm)
REVERT: A  406 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8185 (ttmm)
REVERT: A  433 GLU cc_start: 0.8285 (tt0) cc_final: 0.7723 (mt-10)
REVERT: A  456 MET cc_start: 0.8561 (mmm) cc_final: 0.8295 (mmm)
REVERT: B   82 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8471 (pp)
REVERT: B   91 ASP cc_start: 0.7198 (t0) cc_final: 0.6596 (t70)
REVERT: B  100 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7130 (mmmt)
REVERT: B  132 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7759 (tp-100)
REVERT: I   23 MET cc_start: 0.9030 (mmm) cc_final: 0.7941 (mmm)
REVERT: I   69 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7076 (m-80)
REVERT: C  101 ASP cc_start: 0.7420 (m-30) cc_final: 0.7172 (m-30)
REVERT: C  192 ARG cc_start: 0.7722 (ttm170) cc_final: 0.6938 (mmp80)
REVERT: C  240 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8199 (mmtp)
REVERT: C  243 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8285 (mm)
REVERT: G   56 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7324 (ptm160)
REVERT: G  376 GLU cc_start: 0.7652 (tp30) cc_final: 0.7081 (tt0)
REVERT: G  406 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7645 (tmtt)
REVERT: G  453 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7818 (p)
REVERT: G  456 MET cc_start: 0.7706 (mmm) cc_final: 0.7485 (mmm)
REVERT: G  477 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.5642 (tppt)
  outliers start: 54
  outliers final: 31
  residues processed: 243
  average time/residue: 0.3451
  time to fit residues: 115.8709
Evaluate side-chains
  228 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 190
  time to evaluate  : 2.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   69 TYR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  419 LYS
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  405 GLN
Chi-restraints excluded: chain G residue  453 VAL
Chi-restraints excluded: chain G residue  477 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0470
   chunk 97 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 38 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 152 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A 199 GLN
C 412 ASN
G 195 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.143455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110307 restraints weight = 16147.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.47
r_work: 0.3145 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13544  Z= 0.089
  Angle     :  0.470   6.468  18299  Z= 0.247
  Chirality :  0.040   0.146   1980
  Planarity :  0.003   0.049   2359
  Dihedral  :  6.820  59.765   2023
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.52 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.20), residues: 1633
  helix:  0.95 (0.34), residues: 228
  sheet: -0.04 (0.22), residues: 556
  loop : -1.00 (0.20), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  27 
 HIS   0.002   0.000   HIS A 293 
 PHE   0.011   0.001   PHE C 267 
 TYR   0.012   0.001   TYR B 113 
 ARG   0.005   0.000   ARG C 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  372)
  hydrogen bonds       : angle       4.62903 (  984)
  SS BOND              : bond        0.00218 (   34)
  SS BOND              : angle       0.59583 (   68)
  link_NAG-THR         : bond        0.00131 (    3)
  link_NAG-THR         : angle       1.86938 (    6)
  covalent geometry    : bond        0.00197 (13501)
  covalent geometry    : angle       0.46835 (18225)
  Misc. bond           : bond        0.00043 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 195
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   26 THR cc_start: 0.8473 (p) cc_final: 0.8015 (p)
REVERT: A   77 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7651 (pm20)
REVERT: A  149 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9256 (p)
REVERT: A  192 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8233 (ttm110)
REVERT: A  234 TYR cc_start: 0.7634 (t80) cc_final: 0.7350 (t80)
REVERT: A  250 HIS cc_start: 0.8715 (m-70) cc_final: 0.7929 (t70)
REVERT: A  260 ASP cc_start: 0.8732 (t0) cc_final: 0.8465 (t0)
REVERT: A  369 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8188 (tttm)
REVERT: A  433 GLU cc_start: 0.8184 (tt0) cc_final: 0.7597 (mt-10)
REVERT: B   82 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (pp)
REVERT: B   91 ASP cc_start: 0.7123 (t0) cc_final: 0.6459 (t70)
REVERT: B  100 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7141 (mmmt)
REVERT: B  132 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7598 (tp-100)
REVERT: I   23 MET cc_start: 0.8915 (mmm) cc_final: 0.7975 (mmm)
REVERT: I   69 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7198 (m-80)
REVERT: I   98 GLU cc_start: 0.7570 (tp30) cc_final: 0.7133 (tp30)
REVERT: I  122 LYS cc_start: 0.8608 (tppt) cc_final: 0.8377 (ttmm)
REVERT: C  101 ASP cc_start: 0.7416 (m-30) cc_final: 0.7105 (m-30)
REVERT: C  124 ARG cc_start: 0.7123 (mmp-170) cc_final: 0.6901 (mmp-170)
REVERT: C  182 ILE cc_start: 0.8836 (mt) cc_final: 0.8460 (tt)
REVERT: C  192 ARG cc_start: 0.7521 (ttm170) cc_final: 0.6614 (mmp80)
REVERT: C  240 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8208 (mmtp)
REVERT: G   56 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7413 (ptm160)
REVERT: G  376 GLU cc_start: 0.7734 (tp30) cc_final: 0.6972 (tt0)
REVERT: G  453 VAL cc_start: 0.8133 (t) cc_final: 0.7809 (p)
REVERT: G  456 MET cc_start: 0.7877 (mmm) cc_final: 0.7651 (mmm)
  outliers start: 40
  outliers final: 28
  residues processed: 226
  average time/residue: 0.3775
  time to fit residues: 120.3042
Evaluate side-chains
  216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 2.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   69 TYR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  251 LEU
Chi-restraints excluded: chain G residue  396 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 157 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 199 GLN
C 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.137626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.104705 restraints weight = 16535.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.46
r_work: 0.3029 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  13544  Z= 0.254
  Angle     :  0.614   7.209  18299  Z= 0.325
  Chirality :  0.045   0.156   1980
  Planarity :  0.005   0.053   2359
  Dihedral  :  7.023  59.688   2021
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 13.46 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.20), residues: 1633
  helix:  0.48 (0.34), residues: 225
  sheet: -0.33 (0.22), residues: 546
  loop : -1.28 (0.19), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G  27 
 HIS   0.005   0.001   HIS A 293 
 PHE   0.017   0.002   PHE C 191 
 TYR   0.024   0.002   TYR B 113 
 ARG   0.006   0.001   ARG C 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05434 (  372)
  hydrogen bonds       : angle       4.86853 (  984)
  SS BOND              : bond        0.00531 (   34)
  SS BOND              : angle       1.13049 (   68)
  link_NAG-THR         : bond        0.00227 (    3)
  link_NAG-THR         : angle       2.23995 (    6)
  covalent geometry    : bond        0.00613 (13501)
  covalent geometry    : angle       0.61020 (18225)
  Misc. bond           : bond        0.00064 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 194
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  105 GLN cc_start: 0.7737 (mp10) cc_final: 0.7508 (mp10)
REVERT: A  149 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9281 (p)
REVERT: A  192 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8405 (ttm110)
REVERT: A  234 TYR cc_start: 0.8021 (t80) cc_final: 0.7743 (t80)
REVERT: A  241 MET cc_start: 0.8883 (ttm) cc_final: 0.8636 (ttp)
REVERT: A  250 HIS cc_start: 0.8787 (m-70) cc_final: 0.8568 (m90)
REVERT: A  353 GLU cc_start: 0.7979 (mp0) cc_final: 0.7465 (mp0)
REVERT: A  369 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8192 (tttp)
REVERT: B   62 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7324 (mmtm)
REVERT: B   82 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (pp)
REVERT: B   91 ASP cc_start: 0.7251 (t0) cc_final: 0.6587 (t70)
REVERT: B  100 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7086 (mmmt)
REVERT: B  132 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7886 (tp-100)
REVERT: I  122 LYS cc_start: 0.8589 (tppt) cc_final: 0.8365 (ttmm)
REVERT: I  123 LEU cc_start: 0.8233 (tp) cc_final: 0.7901 (tt)
REVERT: C  101 ASP cc_start: 0.7302 (m-30) cc_final: 0.7044 (m-30)
REVERT: C  124 ARG cc_start: 0.7085 (mmp-170) cc_final: 0.6829 (mmp-170)
REVERT: C  162 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8086 (ptm160)
REVERT: C  192 ARG cc_start: 0.7782 (ttm170) cc_final: 0.6987 (mmt-90)
REVERT: G   56 ARG cc_start: 0.7785 (ptp90) cc_final: 0.7409 (ptm160)
REVERT: G  376 GLU cc_start: 0.7850 (tp30) cc_final: 0.7285 (tt0)
REVERT: G  384 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6450 (tt)
REVERT: G  456 MET cc_start: 0.7865 (mmm) cc_final: 0.7571 (mmm)
REVERT: G  477 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5540 (tppt)
  outliers start: 56
  outliers final: 41
  residues processed: 232
  average time/residue: 0.2852
  time to fit residues: 92.2510
Evaluate side-chains
  237 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 190
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  100 LYS
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   73 LEU
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  162 ARG
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue   40 MET
Chi-restraints excluded: chain G residue   78 ASP
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  250 HIS
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  384 ILE
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  441 VAL
Chi-restraints excluded: chain G residue  453 VAL
Chi-restraints excluded: chain G residue  454 ILE
Chi-restraints excluded: chain G residue  477 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 161 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 127 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0870
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
A 199 GLN
C 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.139419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.106469 restraints weight = 16589.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.48
r_work: 0.3100 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  13544  Z= 0.148
  Angle     :  0.515   7.029  18299  Z= 0.273
  Chirality :  0.042   0.146   1980
  Planarity :  0.004   0.059   2359
  Dihedral  :  6.367  57.713   2021
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 14.14 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.20), residues: 1633
  helix:  0.66 (0.34), residues: 225
  sheet: -0.29 (0.22), residues: 552
  loop : -1.26 (0.19), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G  27 
 HIS   0.003   0.001   HIS I  46 
 PHE   0.010   0.001   PHE A 155 
 TYR   0.019   0.001   TYR B 113 
 ARG   0.007   0.000   ARG G  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04265 (  372)
  hydrogen bonds       : angle       4.68131 (  984)
  SS BOND              : bond        0.00308 (   34)
  SS BOND              : angle       0.78300 (   68)
  link_NAG-THR         : bond        0.00140 (    3)
  link_NAG-THR         : angle       1.87641 (    6)
  covalent geometry    : bond        0.00351 (13501)
  covalent geometry    : angle       0.51295 (18225)
  Misc. bond           : bond        0.00028 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 195
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7214 (mttm)
REVERT: E  105 GLN cc_start: 0.7620 (mp10) cc_final: 0.7296 (mp10)
REVERT: E  107 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7933 (t70)
REVERT: F   46 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.7524 (m90)
REVERT: A   77 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7698 (pm20)
REVERT: A  234 TYR cc_start: 0.7947 (t80) cc_final: 0.7648 (t80)
REVERT: A  241 MET cc_start: 0.8806 (ttm) cc_final: 0.8553 (ttp)
REVERT: A  353 GLU cc_start: 0.7994 (mp0) cc_final: 0.7496 (mp0)
REVERT: A  369 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8242 (tttm)
REVERT: A  469 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5800 (pm20)
REVERT: B   82 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (pp)
REVERT: B   91 ASP cc_start: 0.7164 (t0) cc_final: 0.6508 (t70)
REVERT: B  100 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7081 (mmmt)
REVERT: B  132 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7846 (tp-100)
REVERT: I   98 GLU cc_start: 0.7473 (tp30) cc_final: 0.7108 (tp30)
REVERT: I  122 LYS cc_start: 0.8545 (tppt) cc_final: 0.8314 (ttmm)
REVERT: I  123 LEU cc_start: 0.8236 (tp) cc_final: 0.7892 (tt)
REVERT: C  101 ASP cc_start: 0.7391 (m-30) cc_final: 0.7134 (m-30)
REVERT: C  124 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6868 (mmp-170)
REVERT: C  182 ILE cc_start: 0.8719 (mt) cc_final: 0.8255 (tt)
REVERT: C  192 ARG cc_start: 0.7749 (ttm170) cc_final: 0.6969 (mmp80)
REVERT: G   56 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7436 (ptm160)
REVERT: G  376 GLU cc_start: 0.7722 (tp30) cc_final: 0.7445 (tt0)
REVERT: G  384 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6421 (tt)
REVERT: G  453 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7874 (p)
REVERT: G  456 MET cc_start: 0.7960 (mmm) cc_final: 0.7690 (mmm)
  outliers start: 57
  outliers final: 41
  residues processed: 235
  average time/residue: 0.2967
  time to fit residues: 98.1175
Evaluate side-chains
  239 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 190
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  107 ASP
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   48 ILE
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   73 LEU
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  124 ARG
Chi-restraints excluded: chain C residue  127 GLU
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue   78 ASP
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  250 HIS
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  351 THR
Chi-restraints excluded: chain G residue  362 LEU
Chi-restraints excluded: chain G residue  384 ILE
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  447 CYS
Chi-restraints excluded: chain G residue  453 VAL
Chi-restraints excluded: chain G residue  477 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 148 optimal weight:    3.9990
   chunk 163 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 132 optimal weight:    0.0030
   overall best weight:    0.4750

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
A 199 GLN
C 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.141586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.108587 restraints weight = 16405.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.48
r_work: 0.3079 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13544  Z= 0.085
  Angle     :  0.464   6.745  18299  Z= 0.246
  Chirality :  0.040   0.145   1980
  Planarity :  0.003   0.064   2359
  Dihedral  :  5.814  59.540   2021
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.44 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.20), residues: 1633
  helix:  0.83 (0.34), residues: 228
  sheet: -0.14 (0.22), residues: 552
  loop : -1.17 (0.20), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  27 
 HIS   0.010   0.001   HIS F  46 
 PHE   0.009   0.001   PHE C 267 
 TYR   0.012   0.001   TYR A 137 
 ARG   0.007   0.000   ARG I  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  372)
  hydrogen bonds       : angle       4.49808 (  984)
  SS BOND              : bond        0.00248 (   34)
  SS BOND              : angle       0.56576 (   68)
  link_NAG-THR         : bond        0.00111 (    3)
  link_NAG-THR         : angle       1.71851 (    6)
  covalent geometry    : bond        0.00187 (13501)
  covalent geometry    : angle       0.46233 (18225)
  Misc. bond           : bond        0.00029 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 193
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7646 (pm20)
REVERT: A  199 GLN cc_start: 0.7964 (mt0) cc_final: 0.7625 (mt0)
REVERT: A  234 TYR cc_start: 0.7794 (t80) cc_final: 0.7494 (t80)
REVERT: A  353 GLU cc_start: 0.7956 (mp0) cc_final: 0.7495 (mp0)
REVERT: A  369 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8216 (tttm)
REVERT: B   82 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8551 (pp)
REVERT: B   91 ASP cc_start: 0.7010 (t0) cc_final: 0.6392 (t0)
REVERT: B  100 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7058 (mmmt)
REVERT: B  132 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7710 (tp-100)
REVERT: I   69 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7186 (m-80)
REVERT: I  122 LYS cc_start: 0.8571 (tppt) cc_final: 0.8339 (ttmm)
REVERT: C  101 ASP cc_start: 0.7365 (m-30) cc_final: 0.7039 (m-30)
REVERT: C  124 ARG cc_start: 0.7152 (mmp-170) cc_final: 0.6932 (mmp80)
REVERT: C  162 ARG cc_start: 0.8286 (ptm160) cc_final: 0.8044 (ptm160)
REVERT: C  182 ILE cc_start: 0.8831 (mt) cc_final: 0.8426 (tt)
REVERT: C  192 ARG cc_start: 0.7605 (ttm170) cc_final: 0.6704 (mmp80)
REVERT: G   56 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7392 (ptm160)
REVERT: G  376 GLU cc_start: 0.7739 (tp30) cc_final: 0.7474 (tt0)
REVERT: G  453 VAL cc_start: 0.8180 (t) cc_final: 0.7894 (p)
REVERT: G  456 MET cc_start: 0.7944 (mmm) cc_final: 0.7672 (mmm)
  outliers start: 44
  outliers final: 37
  residues processed: 228
  average time/residue: 0.2742
  time to fit residues: 87.8314
Evaluate side-chains
  226 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   48 ILE
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   69 TYR
Chi-restraints excluded: chain I residue   73 LEU
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  250 HIS
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  351 THR
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  447 CYS
Chi-restraints excluded: chain G residue  477 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 141 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
C 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.107966 restraints weight = 16407.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.47
r_work: 0.3069 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13544  Z= 0.112
  Angle     :  0.479   7.651  18299  Z= 0.254
  Chirality :  0.041   0.143   1980
  Planarity :  0.004   0.052   2359
  Dihedral  :  5.601  59.510   2021
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.16 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.20), residues: 1633
  helix:  0.84 (0.34), residues: 228
  sheet: -0.15 (0.22), residues: 552
  loop : -1.17 (0.20), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  27 
 HIS   0.003   0.001   HIS F  46 
 PHE   0.009   0.001   PHE C 267 
 TYR   0.015   0.001   TYR B 113 
 ARG   0.007   0.000   ARG I  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  372)
  hydrogen bonds       : angle       4.42895 (  984)
  SS BOND              : bond        0.00245 (   34)
  SS BOND              : angle       0.63974 (   68)
  link_NAG-THR         : bond        0.00128 (    3)
  link_NAG-THR         : angle       1.75508 (    6)
  covalent geometry    : bond        0.00263 (13501)
  covalent geometry    : angle       0.47761 (18225)
  Misc. bond           : bond        0.00025 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 190
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7599 (pm20)
REVERT: A  199 GLN cc_start: 0.7831 (mt0) cc_final: 0.7498 (mt0)
REVERT: A  234 TYR cc_start: 0.7851 (t80) cc_final: 0.7535 (t80)
REVERT: A  353 GLU cc_start: 0.7949 (mp0) cc_final: 0.7205 (mp0)
REVERT: A  469 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5785 (pm20)
REVERT: B   62 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7433 (mmtm)
REVERT: B   82 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8557 (pp)
REVERT: B   91 ASP cc_start: 0.7006 (t0) cc_final: 0.6391 (t0)
REVERT: B  100 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7078 (mmmt)
REVERT: B  132 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7640 (tp-100)
REVERT: I   98 GLU cc_start: 0.7605 (tp30) cc_final: 0.7313 (tp30)
REVERT: I  122 LYS cc_start: 0.8561 (tppt) cc_final: 0.8328 (ttmm)
REVERT: C  101 ASP cc_start: 0.7347 (m-30) cc_final: 0.7098 (m-30)
REVERT: C  124 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6866 (mmp80)
REVERT: C  182 ILE cc_start: 0.8821 (mt) cc_final: 0.8408 (tt)
REVERT: C  192 ARG cc_start: 0.7694 (ttm170) cc_final: 0.6861 (mmp80)
REVERT: G   56 ARG cc_start: 0.7785 (ptp90) cc_final: 0.7421 (ptm160)
REVERT: G  376 GLU cc_start: 0.7859 (tp30) cc_final: 0.7585 (tt0)
REVERT: G  384 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6323 (tt)
REVERT: G  406 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7673 (tmtt)
REVERT: G  453 VAL cc_start: 0.8203 (t) cc_final: 0.7910 (p)
REVERT: G  456 MET cc_start: 0.7951 (mmm) cc_final: 0.7700 (mmm)
  outliers start: 54
  outliers final: 43
  residues processed: 227
  average time/residue: 0.2860
  time to fit residues: 91.2433
Evaluate side-chains
  234 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 185
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   48 ILE
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   73 LEU
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  124 ARG
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  250 HIS
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  351 THR
Chi-restraints excluded: chain G residue  362 LEU
Chi-restraints excluded: chain G residue  384 ILE
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  406 LYS
Chi-restraints excluded: chain G residue  447 CYS
Chi-restraints excluded: chain G residue  477 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0870
   chunk 138 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 104 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
C 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.142339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109569 restraints weight = 16185.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.47
r_work: 0.3144 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13544  Z= 0.085
  Angle     :  0.452   7.543  18299  Z= 0.239
  Chirality :  0.040   0.140   1980
  Planarity :  0.003   0.051   2359
  Dihedral  :  5.299  57.830   2021
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.98 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.20), residues: 1633
  helix:  1.45 (0.35), residues: 210
  sheet: -0.04 (0.22), residues: 528
  loop : -0.98 (0.19), residues: 895

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  27 
 HIS   0.002   0.000   HIS I  46 
 PHE   0.011   0.001   PHE C 267 
 TYR   0.012   0.001   TYR A 137 
 ARG   0.007   0.000   ARG I  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  372)
  hydrogen bonds       : angle       4.31636 (  984)
  SS BOND              : bond        0.00194 (   34)
  SS BOND              : angle       0.50212 (   68)
  link_NAG-THR         : bond        0.00091 (    3)
  link_NAG-THR         : angle       1.65170 (    6)
  covalent geometry    : bond        0.00195 (13501)
  covalent geometry    : angle       0.45045 (18225)
  Misc. bond           : bond        0.00015 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 184
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7615 (pm20)
REVERT: A  199 GLN cc_start: 0.7975 (mt0) cc_final: 0.7671 (mt0)
REVERT: A  234 TYR cc_start: 0.7755 (t80) cc_final: 0.7441 (t80)
REVERT: A  353 GLU cc_start: 0.7964 (mp0) cc_final: 0.7515 (mp0)
REVERT: A  469 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5638 (pm20)
REVERT: B   62 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7454 (mmtm)
REVERT: B   82 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8556 (pp)
REVERT: B   91 ASP cc_start: 0.6932 (t0) cc_final: 0.6287 (t70)
REVERT: B  100 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7125 (mmmt)
REVERT: B  132 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7634 (tp-100)
REVERT: I   69 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7130 (m-80)
REVERT: I   98 GLU cc_start: 0.7341 (tp30) cc_final: 0.7115 (tp30)
REVERT: I  122 LYS cc_start: 0.8568 (tppt) cc_final: 0.8338 (ttmm)
REVERT: C  101 ASP cc_start: 0.7318 (m-30) cc_final: 0.7018 (m-30)
REVERT: C  124 ARG cc_start: 0.7025 (mmp-170) cc_final: 0.6783 (mmp80)
REVERT: C  182 ILE cc_start: 0.8854 (mt) cc_final: 0.8479 (tt)
REVERT: C  192 ARG cc_start: 0.7597 (ttm170) cc_final: 0.6727 (mmp80)
REVERT: C  197 GLU cc_start: 0.8336 (pt0) cc_final: 0.7828 (mt-10)
REVERT: G   56 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7502 (ptm160)
REVERT: G  376 GLU cc_start: 0.7833 (tp30) cc_final: 0.7574 (tt0)
REVERT: G  406 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7640 (tmtt)
REVERT: G  453 VAL cc_start: 0.8203 (t) cc_final: 0.7916 (p)
REVERT: G  456 MET cc_start: 0.7974 (mmm) cc_final: 0.7722 (mmm)
  outliers start: 45
  outliers final: 37
  residues processed: 217
  average time/residue: 0.2867
  time to fit residues: 87.4335
Evaluate side-chains
  223 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 181
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  100 LYS
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   48 ILE
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   69 TYR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  127 GLU
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  406 LYS
Chi-restraints excluded: chain G residue  454 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 87 optimal weight:    0.0040
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0070
   chunk 95 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.5010

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
C 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.142393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109684 restraints weight = 16267.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.47
r_work: 0.3133 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13544  Z= 0.085
  Angle     :  0.458   7.471  18299  Z= 0.243
  Chirality :  0.040   0.141   1980
  Planarity :  0.003   0.049   2359
  Dihedral  :  5.188  57.435   2019
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.33 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.20), residues: 1633
  helix:  1.52 (0.35), residues: 210
  sheet: -0.22 (0.21), residues: 582
  loop : -1.07 (0.20), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  27 
 HIS   0.002   0.000   HIS I  46 
 PHE   0.010   0.001   PHE C 267 
 TYR   0.012   0.001   TYR A 137 
 ARG   0.007   0.000   ARG I  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  372)
  hydrogen bonds       : angle       4.26954 (  984)
  SS BOND              : bond        0.00195 (   34)
  SS BOND              : angle       0.48840 (   68)
  link_NAG-THR         : bond        0.00111 (    3)
  link_NAG-THR         : angle       1.68189 (    6)
  covalent geometry    : bond        0.00192 (13501)
  covalent geometry    : angle       0.45683 (18225)
  Misc. bond           : bond        0.00012 (    6)

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

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

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3266 Ramachandran restraints generated.
    1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 185
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7615 (pm20)
REVERT: A  199 GLN cc_start: 0.7971 (mt0) cc_final: 0.7673 (mt0)
REVERT: A  234 TYR cc_start: 0.7699 (t80) cc_final: 0.7393 (t80)
REVERT: A  353 GLU cc_start: 0.7962 (mp0) cc_final: 0.7204 (mp0)
REVERT: A  469 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5619 (pm20)
REVERT: B   62 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7397 (mmtm)
REVERT: B   82 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8488 (pp)
REVERT: B   91 ASP cc_start: 0.6888 (t0) cc_final: 0.6279 (t0)
REVERT: B  105 GLN cc_start: 0.7905 (mt0) cc_final: 0.7248 (mp-120)
REVERT: B  132 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7633 (tp-100)
REVERT: I   69 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7142 (m-80)
REVERT: I   98 GLU cc_start: 0.7492 (tp30) cc_final: 0.7062 (tp30)
REVERT: I  122 LYS cc_start: 0.8556 (tppt) cc_final: 0.8330 (ttmm)
REVERT: C  101 ASP cc_start: 0.7304 (m-30) cc_final: 0.7007 (m-30)
REVERT: C  124 ARG cc_start: 0.6848 (mmp-170) cc_final: 0.6638 (mmp80)
REVERT: C  182 ILE cc_start: 0.8825 (mt) cc_final: 0.8460 (tt)
REVERT: C  192 ARG cc_start: 0.7589 (ttm170) cc_final: 0.6705 (mmp80)
REVERT: C  197 GLU cc_start: 0.8300 (pt0) cc_final: 0.7746 (mt-10)
REVERT: G   56 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7494 (ptm160)
REVERT: G  376 GLU cc_start: 0.7782 (tp30) cc_final: 0.7502 (tt0)
REVERT: G  406 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7611 (tmtt)
REVERT: G  453 VAL cc_start: 0.8247 (t) cc_final: 0.7957 (p)
REVERT: G  456 MET cc_start: 0.7963 (mmm) cc_final: 0.7706 (mmm)
  outliers start: 41
  outliers final: 36
  residues processed: 213
  average time/residue: 0.2849
  time to fit residues: 85.0854
Evaluate side-chains
  227 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 187
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  120 TYR
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  405 GLN
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  120 TYR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   52 LEU
Chi-restraints excluded: chain I residue   69 TYR
Chi-restraints excluded: chain I residue  116 THR
Chi-restraints excluded: chain C residue   25 SER
Chi-restraints excluded: chain C residue  127 GLU
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  452 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  461 LEU
Chi-restraints excluded: chain C residue  471 ILE
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   25 SER
Chi-restraints excluded: chain G residue  193 THR
Chi-restraints excluded: chain G residue  265 THR
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  406 LYS
Chi-restraints excluded: chain G residue  454 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 144 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  46 HIS
C 412 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.137461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.104569 restraints weight = 16496.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.49
r_work: 0.3088 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13544  Z= 0.203
  Angle     :  0.562   7.335  18299  Z= 0.299
  Chirality :  0.043   0.147   1980
  Planarity :  0.004   0.061   2359
  Dihedral  :  5.696  58.166   2015
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.19 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.20), residues: 1633
  helix:  0.71 (0.34), residues: 225
  sheet: -0.21 (0.22), residues: 546
  loop : -1.25 (0.19), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G  27 
 HIS   0.004   0.001   HIS I  46 
 PHE   0.013   0.002   PHE C 191 
 TYR   0.019   0.002   TYR B 113 
 ARG   0.007   0.001   ARG I  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  372)
  hydrogen bonds       : angle       4.54654 (  984)
  SS BOND              : bond        0.00367 (   34)
  SS BOND              : angle       0.90618 (   68)
  link_NAG-THR         : bond        0.00135 (    3)
  link_NAG-THR         : angle       1.82170 (    6)
  covalent geometry    : bond        0.00491 (13501)
  covalent geometry    : angle       0.55905 (18225)
  Misc. bond           : bond        0.00047 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7528.66 seconds
wall clock time: 135 minutes 36.03 seconds (8136.03 seconds total)