Starting phenix.real_space_refine
on Sat Aug 23 01:36:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i0q_35106/08_2025/8i0q_35106.map"
  }
  resolution = 4.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      30      5.16       5
     C    5601      2.51       5
     N    1489      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8842
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2683
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 194
          Unresolved non-hydrogen angles: 231
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 2, 'ARG:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 130
    Chain: "B"
      Number of atoms: 2679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2679
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 236
          Unresolved non-hydrogen dihedrals: 168
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 15, 'TYR:plan': 2, 'ARG:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 134
    Chain: "H"
      Number of atoms: 892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 892
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "I"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 893
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "L"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 769
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 17
    Chain: "M"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 773
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "U"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 79
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "V"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 74
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 2.39, per 1000 atoms: 0.27
  Number of scatterers: 8842
  At special positions: 0
  Unit cell: (130.058, 153.106, 85.6076, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P      10     15.00
     O    1712      8.00
     N    1489      7.00
     C    5601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 366.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2232

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 24 sheets defined
      7.7% alpha, 43.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 94
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 278 through 282
      removed outlier: 3.876A  pdb=" N   ARG A 282 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.893A  pdb=" N   ASN A 311 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 339
      removed outlier: 3.805A  pdb=" N   ALA A 339 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 94
    Processing helix  chain 'B' and resid 98 through 109
      removed outlier: 3.605A  pdb=" N   GLU B 102 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 282
      removed outlier: 3.896A  pdb=" N   ARG B 282 " --> pdb=" O   ALA B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.931A  pdb=" N   ASN B 311 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 339
      removed outlier: 3.539A  pdb=" N   LEU B 338 " --> pdb=" O   LEU B 335 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA B 339 " --> pdb=" O   GLY B 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 335 through 339'
    Processing helix  chain 'H' and resid 65 through 68
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'I' and resid 65 through 68
    Processing helix  chain 'I' and resid 90 through 94
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'M' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118
      removed outlier: 4.196A  pdb=" N   VAL A  40 " --> pdb=" O   TYR A  21 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A  21 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A  22 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 4.090A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG A  62 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP A 143 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL A  53 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE A  61 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ASP A  78 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   TYR A  63 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ARG A  76 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28
      removed outlier: 4.090A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188
    Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 258
      removed outlier: 5.481A  pdb=" N   GLN A 248 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   ILE A 241 " --> pdb=" O   GLN A 248 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA A 254 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL A 328 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE A 231 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LYS A 326 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   ILE A 233 " --> pdb=" O   LYS A 324 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LYS A 324 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   VAL A 235 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LYS A 322 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLN A 237 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   SER A 320 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE A 318 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 118
      removed outlier: 4.213A  pdb=" N   VAL B  40 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR B  21 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 29
      removed outlier: 4.048A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.211A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG B  62 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP B 143 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL B  53 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   PHE B  61 " --> pdb=" O   ASP B  78 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ASP B  78 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 8.326A  pdb=" N   TYR B  63 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   ARG B  76 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29
      removed outlier: 4.048A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.211A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 183 through 188
    Processing sheet with id=AB1, first strand: chain 'B' and resid 246 through 258
      removed outlier: 5.531A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 254 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL B 328 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ILE B 231 " --> pdb=" O   LYS B 326 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LYS B 326 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   ILE B 233 " --> pdb=" O   LYS B 324 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LYS B 324 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   VAL B 235 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS B 322 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   GLN B 237 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   SER B 320 " --> pdb=" O   GLN B 237 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ALA B 239 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE B 318 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 8 through 10
      removed outlier: 3.895A  pdb=" N   LEU H  23 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 14 through 15
    Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 63
      removed outlier: 3.581A  pdb=" N   TYR H  62 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA H 100 " --> pdb=" O   HIS H  38 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL H  40 " --> pdb=" O   TYR H  98 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 61 through 63
      removed outlier: 3.581A  pdb=" N   TYR H  62 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA H 100 " --> pdb=" O   HIS H  38 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL H  40 " --> pdb=" O   TYR H  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 8 through 10
      removed outlier: 3.852A  pdb=" N   LEU I  23 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR I  81 " --> pdb=" O   ASP I  76 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 14 through 15
    Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 63
      removed outlier: 3.625A  pdb=" N   TYR I  62 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS I  38 " --> pdb=" O   ALA I 100 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ALA I 100 " --> pdb=" O   HIS I  38 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL I  40 " --> pdb=" O   TYR I  98 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   TYR I 112 " --> pdb=" O   ARG I 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 61 through 63
      removed outlier: 3.625A  pdb=" N   TYR I  62 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS I  38 " --> pdb=" O   ALA I 100 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ALA I 100 " --> pdb=" O   HIS I  38 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL I  40 " --> pdb=" O   TYR I  98 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 6 through 8
      removed outlier: 3.537A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.362A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.498A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'M' and resid 5 through 8
      removed outlier: 3.519A  pdb=" N   VAL M  20 " --> pdb=" O   ILE M  76 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 13
      removed outlier: 6.293A  pdb=" N   LEU M  12 " --> pdb=" O   GLU M 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'M' and resid 54 through 55
      removed outlier: 6.557A  pdb=" N   TRP M  36 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   TYR M  50 " --> pdb=" O   VAL M  34 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL M  34 " --> pdb=" O   TYR M  50 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    792 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: 1.41

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2858
        1.34 -     1.46: 2084
        1.46 -     1.58: 4026
        1.58 -     1.69: 37
        1.69 -     1.81: 38
  Bond restraints: 9043
  Sorted by residual:
  bond pdb=" O2P SEP V 351 "
       pdb=" P   SEP V 351 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" O3P SEP V 351 "
       pdb=" P   SEP V 351 "
    ideal  model  delta    sigma   weight residual
    1.610  1.515  0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" O1P SEP V 351 "
       pdb=" P   SEP V 351 "
    ideal  model  delta    sigma   weight residual
    1.610  1.516  0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C   MET B 352 "
       pdb=" N   HIS B 353 "
    ideal  model  delta    sigma   weight residual
    1.331  1.381 -0.050 2.83e-02 1.25e+03 3.06e+00
  bond pdb=" C   MET A 352 "
       pdb=" N   HIS A 353 "
    ideal  model  delta    sigma   weight residual
    1.331  1.380 -0.049 2.83e-02 1.25e+03 3.03e+00
  ... (remaining 9038 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 12088
        1.68 -     3.36: 241
        3.36 -     5.04: 41
        5.04 -     6.71: 2
        6.71 -     8.39: 1
  Bond angle restraints: 12373
  Sorted by residual:
  angle pdb=" C   GLU B 308 "
        pdb=" CA  GLU B 308 "
        pdb=" CB  GLU B 308 "
      ideal   model   delta    sigma   weight residual
     115.79  110.62    5.17 1.19e+00 7.06e-01 1.89e+01
  angle pdb=" N   ARG A 103 "
        pdb=" CA  ARG A 103 "
        pdb=" C   ARG A 103 "
      ideal   model   delta    sigma   weight residual
     111.02  106.97    4.05 1.22e+00 6.72e-01 1.10e+01
  angle pdb=" CB  SEP V 351 "
        pdb=" OG  SEP V 351 "
        pdb=" P   SEP V 351 "
      ideal   model   delta    sigma   weight residual
     110.00  118.39   -8.39 3.00e+00 1.11e-01 7.83e+00
  angle pdb=" O   ARG A 103 "
        pdb=" C   ARG A 103 "
        pdb=" N   LEU A 104 "
      ideal   model   delta    sigma   weight residual
     122.08  124.67   -2.59 1.07e+00 8.73e-01 5.84e+00
  angle pdb=" N   PHE B 149 "
        pdb=" CA  PHE B 149 "
        pdb=" C   PHE B 149 "
      ideal   model   delta    sigma   weight residual
     107.73  110.83   -3.10 1.34e+00 5.57e-01 5.36e+00
  ... (remaining 12368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 4986
       16.96 -    33.91: 334
       33.91 -    50.87: 52
       50.87 -    67.83: 11
       67.83 -    84.79: 12
  Dihedral angle restraints: 5395
    sinusoidal: 1923
      harmonic: 3472
  Sorted by residual:
  dihedral pdb=" CA  GLN L   4 "
           pdb=" C   GLN L   4 "
           pdb=" N   MET L   5 "
           pdb=" CA  MET L   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.43  -21.57     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  PHE B 190 "
           pdb=" C   PHE B 190 "
           pdb=" N   LEU B 191 "
           pdb=" CA  LEU B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.36  -18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE A 190 "
           pdb=" C   PHE A 190 "
           pdb=" N   LEU A 191 "
           pdb=" CA  LEU A 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.81  -17.19     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 5392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 877
       0.029 -    0.058: 381
       0.058 -    0.088: 52
       0.088 -    0.117: 100
       0.117 -    0.146: 26
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" CA  ILE A 241 "
            pdb=" N   ILE A 241 "
            pdb=" C   ILE A 241 "
            pdb=" CB  ILE A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  VAL A 343 "
            pdb=" N   VAL A 343 "
            pdb=" C   VAL A 343 "
            pdb=" CB  VAL A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  VAL B 345 "
            pdb=" N   VAL B 345 "
            pdb=" C   VAL B 345 "
            pdb=" CB  VAL B 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 275 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO B 276 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 276 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 276 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 275 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO A 276 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 276 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 276 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN I  16 "    0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO I  17 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO I  17 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO I  17 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 552
        2.71 -     3.26: 9440
        3.26 -     3.81: 14042
        3.81 -     4.35: 16614
        4.35 -     4.90: 27916
  Nonbonded interactions: 68564
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 172 "
            pdb=" O   TYR B 173 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" NZ  LYS A 107 "
            pdb=" O1P SEP V 347 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   GLN I   6 "
            pdb=" OG  SER I  28 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" ND2 ASN A 222 "
            pdb=" O   ALA A 263 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" NE  ARG B  62 "
            pdb=" OG1 THR B  74 "
     model   vdw
     2.236 3.120
  ... (remaining 68559 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 133 or (resid 134 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 135 through 368))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'H'
  selection = (chain 'I' and (resid 5 through 27 or (resid 28 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 29 through 122))
}
ncs_group {
  reference = chain 'L'
  selection = (chain 'M' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 92 through 106))
}
ncs_group {
  reference = (chain 'U' and (resid 343 through 349 or (resid 350 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 351))
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.930
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
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      :  0.003   0.096   9047  Z= 0.165
  Angle     :  0.593   8.393  12381  Z= 0.329
  Chirality :  0.043   0.146   1436
  Planarity :  0.004   0.047   1587
  Dihedral  : 12.560  84.785   3151
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.25), residues: 1162
  helix: -1.43 (1.04), residues: 22
  sheet: -1.01 (0.23), residues: 464
  loop : -0.79 (0.25), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 101 
 TYR   0.008   0.001   TYR B 113 
 PHE   0.009   0.001   PHE L  72 
 TRP   0.003   0.001   TRP H 106 
 HIS   0.004   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9043)
  covalent geometry    : angle       0.59274 (12373)
  SS BOND              : bond        0.00152 (    4)
  SS BOND              : angle       0.32277 (    8)
  hydrogen bonds       : bond        0.28745 (  287)
  hydrogen bonds       : angle      10.88663 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    7 LEU cc_start: 0.6995 (pt) cc_final: 0.6702 (pp)
REVERT: H   21 LEU cc_start: 0.9417 (mt) cc_final: 0.9197 (mp)
REVERT: H   86 MET cc_start: 0.7768 (pmm) cc_final: 0.7361 (pmm)
REVERT: I    7 LEU cc_start: 0.7424 (pt) cc_final: 0.7080 (pp)
REVERT: I   21 LEU cc_start: 0.9413 (mt) cc_final: 0.9194 (mp)
REVERT: I   86 MET cc_start: 0.7567 (pmm) cc_final: 0.7110 (pmm)
REVERT: L    5 MET cc_start: 0.7409 (ttt) cc_final: 0.6658 (pmm)
REVERT: L  101 GLN cc_start: 0.8947 (mp10) cc_final: 0.8647 (pm20)
REVERT: M    5 MET cc_start: 0.7713 (ttp) cc_final: 0.6691 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0721
  time to fit residues: 4.8512
Evaluate side-chains
  29 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0070
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    2.4006

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
B 219 HIS
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** M   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.037378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.030226 restraints weight = 90019.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.031143 restraints weight = 57031.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.031788 restraints weight = 41371.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.032261 restraints weight = 32782.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.032589 restraints weight = 27535.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9047  Z= 0.199
  Angle     :  0.665   5.434  12381  Z= 0.347
  Chirality :  0.044   0.151   1436
  Planarity :  0.004   0.033   1587
  Dihedral  :  8.098  88.650   1314
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1162
  helix: -1.10 (0.98), residues: 24
  sheet: -1.01 (0.23), residues: 466
  loop : -0.56 (0.26), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG M  62 
 TYR   0.020   0.002   TYR I 107 
 PHE   0.019   0.003   PHE B 190 
 TRP   0.016   0.002   TRP H  39 
 HIS   0.008   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9043)
  covalent geometry    : angle       0.66505 (12373)
  SS BOND              : bond        0.00790 (    4)
  SS BOND              : angle       0.78559 (    8)
  hydrogen bonds       : bond        0.04259 (  287)
  hydrogen bonds       : angle       7.06795 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8126 (p) cc_final: 0.7724 (p)
REVERT: A  352 MET cc_start: 0.8868 (ptm) cc_final: 0.8055 (ptm)
REVERT: B  150 CYS cc_start: 0.8409 (p) cc_final: 0.7893 (p)
REVERT: H   21 LEU cc_start: 0.9431 (mt) cc_final: 0.9171 (tp)
REVERT: H   86 MET cc_start: 0.7733 (pmm) cc_final: 0.7466 (pmm)
REVERT: I   21 LEU cc_start: 0.9530 (mt) cc_final: 0.9198 (tp)
REVERT: I   86 MET cc_start: 0.7731 (pmm) cc_final: 0.7445 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0710
  time to fit residues: 4.2744
Evaluate side-chains
  27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   4 GLN
M   7 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.037188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.030138 restraints weight = 90568.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.031058 restraints weight = 56642.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.031718 restraints weight = 40850.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.032185 restraints weight = 32239.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032525 restraints weight = 27063.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9047  Z= 0.190
  Angle     :  0.642   8.483  12381  Z= 0.334
  Chirality :  0.043   0.148   1436
  Planarity :  0.004   0.033   1587
  Dihedral  :  8.038  83.339   1314
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.35 %
    Favored  : 94.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.25), residues: 1162
  helix: -0.95 (0.99), residues: 24
  sheet: -0.97 (0.22), residues: 474
  loop : -0.51 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  70 
 TYR   0.017   0.002   TYR H 107 
 PHE   0.019   0.002   PHE A 190 
 TRP   0.013   0.002   TRP H  39 
 HIS   0.007   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9043)
  covalent geometry    : angle       0.64194 (12373)
  SS BOND              : bond        0.00635 (    4)
  SS BOND              : angle       0.56995 (    8)
  hydrogen bonds       : bond        0.03853 (  287)
  hydrogen bonds       : angle       6.65933 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8130 (p) cc_final: 0.7826 (p)
REVERT: A  352 MET cc_start: 0.8512 (ptm) cc_final: 0.7610 (ptm)
REVERT: B  150 CYS cc_start: 0.8176 (p) cc_final: 0.7810 (p)
REVERT: I   86 MET cc_start: 0.8335 (pmm) cc_final: 0.8123 (pmm)
  outliers start: 3
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0636
  time to fit residues: 3.9247
Evaluate side-chains
  25 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.037587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.030453 restraints weight = 91136.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.031394 restraints weight = 57175.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.032059 restraints weight = 41357.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.032511 restraints weight = 32693.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.032858 restraints weight = 27598.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9047  Z= 0.150
  Angle     :  0.598   7.062  12381  Z= 0.306
  Chirality :  0.043   0.159   1436
  Planarity :  0.004   0.034   1587
  Dihedral  :  7.834  82.508   1314
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.25), residues: 1162
  helix: -0.61 (1.05), residues: 24
  sheet: -0.81 (0.23), residues: 474
  loop : -0.49 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  90 
 TYR   0.011   0.001   TYR H 107 
 PHE   0.013   0.002   PHE L  72 
 TRP   0.011   0.002   TRP H  39 
 HIS   0.005   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9043)
  covalent geometry    : angle       0.59771 (12373)
  SS BOND              : bond        0.00519 (    4)
  SS BOND              : angle       0.34383 (    8)
  hydrogen bonds       : bond        0.03269 (  287)
  hydrogen bonds       : angle       6.25640 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  150 CYS cc_start: 0.8180 (p) cc_final: 0.7832 (p)
REVERT: A  352 MET cc_start: 0.8396 (ptm) cc_final: 0.7337 (ptm)
REVERT: B  150 CYS cc_start: 0.8085 (p) cc_final: 0.7661 (p)
REVERT: H   86 MET cc_start: 0.8339 (pmm) cc_final: 0.8062 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0707
  time to fit residues: 4.1366
Evaluate side-chains
  22 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 85 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0770
   chunk 60 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.2542

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.038293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.030980 restraints weight = 87883.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.031927 restraints weight = 55981.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.032608 restraints weight = 40732.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.033094 restraints weight = 32296.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.033430 restraints weight = 27111.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9047  Z= 0.116
  Angle     :  0.561   5.197  12381  Z= 0.283
  Chirality :  0.042   0.158   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  7.527  83.437   1314
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.25), residues: 1162
  helix: -0.11 (1.12), residues: 24
  sheet: -0.67 (0.23), residues: 484
  loop : -0.45 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  90 
 TYR   0.009   0.001   TYR H 107 
 PHE   0.012   0.002   PHE L  72 
 TRP   0.008   0.001   TRP H  39 
 HIS   0.004   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9043)
  covalent geometry    : angle       0.56154 (12373)
  SS BOND              : bond        0.00547 (    4)
  SS BOND              : angle       0.24318 (    8)
  hydrogen bonds       : bond        0.02902 (  287)
  hydrogen bonds       : angle       5.74190 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8076 (p) cc_final: 0.7752 (p)
REVERT: A  352 MET cc_start: 0.8312 (ptm) cc_final: 0.7215 (ptm)
REVERT: B  150 CYS cc_start: 0.7933 (p) cc_final: 0.7462 (p)
REVERT: L   43 LYS cc_start: 0.9493 (mtmm) cc_final: 0.9291 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0793
  time to fit residues: 4.6151
Evaluate side-chains
  25 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0060
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 66 optimal weight:    0.3980
   chunk 95 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 110 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.0802

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.038834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031396 restraints weight = 88745.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.032342 restraints weight = 56783.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033034 restraints weight = 41434.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.033482 restraints weight = 32910.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.033858 restraints weight = 27868.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9047  Z= 0.105
  Angle     :  0.539   5.061  12381  Z= 0.270
  Chirality :  0.042   0.153   1436
  Planarity :  0.004   0.028   1587
  Dihedral  :  7.330  83.933   1314
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.25), residues: 1162
  helix: -0.02 (1.08), residues: 24
  sheet: -0.51 (0.23), residues: 484
  loop : -0.41 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 101 
 TYR   0.011   0.001   TYR I 107 
 PHE   0.012   0.002   PHE L  72 
 TRP   0.007   0.001   TRP H  39 
 HIS   0.003   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9043)
  covalent geometry    : angle       0.53963 (12373)
  SS BOND              : bond        0.00518 (    4)
  SS BOND              : angle       0.24382 (    8)
  hydrogen bonds       : bond        0.02725 (  287)
  hydrogen bonds       : angle       5.44685 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  150 CYS cc_start: 0.7994 (p) cc_final: 0.7663 (p)
REVERT: A  352 MET cc_start: 0.8399 (ptm) cc_final: 0.7284 (ptm)
REVERT: B  150 CYS cc_start: 0.7838 (p) cc_final: 0.7407 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0897
  time to fit residues: 5.4265
Evaluate side-chains
  26 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.039146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.031600 restraints weight = 87303.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.032535 restraints weight = 56246.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.033212 restraints weight = 41311.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.033679 restraints weight = 32887.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.034034 restraints weight = 27850.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9047  Z= 0.095
  Angle     :  0.530   4.992  12381  Z= 0.263
  Chirality :  0.042   0.151   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  7.185  84.376   1314
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.25), residues: 1162
  helix:  0.27 (1.05), residues: 24
  sheet: -0.36 (0.23), residues: 480
  loop : -0.36 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  62 
 TYR   0.007   0.001   TYR A 113 
 PHE   0.011   0.001   PHE L  72 
 TRP   0.005   0.001   TRP H  39 
 HIS   0.003   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 9043)
  covalent geometry    : angle       0.52986 (12373)
  SS BOND              : bond        0.00497 (    4)
  SS BOND              : angle       0.19947 (    8)
  hydrogen bonds       : bond        0.02565 (  287)
  hydrogen bonds       : angle       5.19049 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.9078 (p90) cc_final: 0.8767 (p90)
REVERT: A  150 CYS cc_start: 0.7915 (p) cc_final: 0.7310 (p)
REVERT: A  352 MET cc_start: 0.8630 (ptm) cc_final: 0.7585 (ptm)
REVERT: B  150 CYS cc_start: 0.7792 (p) cc_final: 0.7377 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0877
  time to fit residues: 5.3739
Evaluate side-chains
  25 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.038476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.031199 restraints weight = 91843.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.032132 restraints weight = 58152.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032789 restraints weight = 42172.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.033267 restraints weight = 33372.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.033591 restraints weight = 28001.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9047  Z= 0.135
  Angle     :  0.557   5.018  12381  Z= 0.282
  Chirality :  0.042   0.147   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  7.333  84.106   1314
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.25), residues: 1162
  helix:  0.37 (1.08), residues: 24
  sheet: -0.46 (0.23), residues: 480
  loop : -0.39 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 103 
 TYR   0.012   0.001   TYR I 107 
 PHE   0.034   0.002   PHE H 105 
 TRP   0.011   0.001   TRP H  39 
 HIS   0.004   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9043)
  covalent geometry    : angle       0.55694 (12373)
  SS BOND              : bond        0.00537 (    4)
  SS BOND              : angle       0.22752 (    8)
  hydrogen bonds       : bond        0.02858 (  287)
  hydrogen bonds       : angle       5.39533 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8013 (p) cc_final: 0.7641 (p)
REVERT: A  352 MET cc_start: 0.8230 (ptm) cc_final: 0.7188 (ptm)
REVERT: B  150 CYS cc_start: 0.7807 (p) cc_final: 0.7319 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0781
  time to fit residues: 4.4640
Evaluate side-chains
  21 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0980
   chunk 107 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.038969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.031561 restraints weight = 89916.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032492 restraints weight = 57281.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.033162 restraints weight = 41694.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.033617 restraints weight = 33064.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.033986 restraints weight = 27969.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9047  Z= 0.098
  Angle     :  0.523   4.992  12381  Z= 0.263
  Chirality :  0.042   0.149   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  7.151  85.007   1314
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1162
  helix:  0.74 (1.08), residues: 24
  sheet: -0.45 (0.23), residues: 490
  loop : -0.26 (0.26), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  90 
 TYR   0.008   0.001   TYR B 173 
 PHE   0.030   0.002   PHE H 105 
 TRP   0.005   0.001   TRP M  36 
 HIS   0.003   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 9043)
  covalent geometry    : angle       0.52296 (12373)
  SS BOND              : bond        0.00508 (    4)
  SS BOND              : angle       0.26376 (    8)
  hydrogen bonds       : bond        0.02527 (  287)
  hydrogen bonds       : angle       5.10484 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.9156 (p90) cc_final: 0.8840 (p90)
REVERT: A  150 CYS cc_start: 0.7915 (p) cc_final: 0.7268 (p)
REVERT: A  352 MET cc_start: 0.8667 (ptm) cc_final: 0.7588 (ptm)
REVERT: B  150 CYS cc_start: 0.7885 (p) cc_final: 0.7478 (p)
REVERT: B  352 MET cc_start: 0.8876 (ppp) cc_final: 0.8614 (ppp)
REVERT: I   84 LEU cc_start: 0.8818 (mm) cc_final: 0.8517 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0743
  time to fit residues: 4.6653
Evaluate side-chains
  24 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 95 optimal weight:    7.9990
   chunk 109 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.039589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032097 restraints weight = 88913.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033027 restraints weight = 56994.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.033674 restraints weight = 41619.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.034162 restraints weight = 33191.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.034478 restraints weight = 27904.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9047  Z= 0.084
  Angle     :  0.512   5.008  12381  Z= 0.253
  Chirality :  0.042   0.148   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  6.937  85.059   1314
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.25), residues: 1162
  helix:  0.97 (1.09), residues: 24
  sheet: -0.22 (0.23), residues: 486
  loop : -0.29 (0.26), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  90 
 TYR   0.006   0.001   TYR A 113 
 PHE   0.026   0.001   PHE H 105 
 TRP   0.006   0.001   TRP M  36 
 HIS   0.003   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 9043)
  covalent geometry    : angle       0.51251 (12373)
  SS BOND              : bond        0.00485 (    4)
  SS BOND              : angle       0.26051 (    8)
  hydrogen bonds       : bond        0.02400 (  287)
  hydrogen bonds       : angle       4.84152 (  792)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.9072 (p90) cc_final: 0.8727 (p90)
REVERT: A  150 CYS cc_start: 0.7787 (p) cc_final: 0.7160 (p)
REVERT: A  352 MET cc_start: 0.8598 (ptm) cc_final: 0.7818 (ptm)
REVERT: B  150 CYS cc_start: 0.7693 (p) cc_final: 0.7275 (p)
REVERT: H   21 LEU cc_start: 0.9329 (pt) cc_final: 0.9048 (pt)
REVERT: I   84 LEU cc_start: 0.8851 (mm) cc_final: 0.8392 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0740
  time to fit residues: 5.1257
Evaluate side-chains
  28 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.038284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.030967 restraints weight = 91892.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.031887 restraints weight = 58228.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.032543 restraints weight = 42307.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.032991 restraints weight = 33518.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.033344 restraints weight = 28350.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9047  Z= 0.140
  Angle     :  0.557   5.074  12381  Z= 0.282
  Chirality :  0.042   0.142   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  7.147  84.055   1314
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.25), residues: 1162
  helix:  0.73 (1.08), residues: 24
  sheet: -0.47 (0.23), residues: 490
  loop : -0.34 (0.26), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  90 
 TYR   0.012   0.001   TYR H 107 
 PHE   0.025   0.002   PHE H 105 
 TRP   0.012   0.002   TRP H  39 
 HIS   0.005   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9043)
  covalent geometry    : angle       0.55695 (12373)
  SS BOND              : bond        0.00533 (    4)
  SS BOND              : angle       0.24089 (    8)
  hydrogen bonds       : bond        0.02854 (  287)
  hydrogen bonds       : angle       5.14176 (  792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1350.01 seconds
wall clock time: 24 minutes 14.02 seconds (1454.02 seconds total)