Starting phenix.real_space_refine
on Tue Apr 29 22:57:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i0q_35106/04_2025/8i0q_35106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i0q_35106/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i0q_35106/04_2025/8i0q_35106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i0q_35106/04_2025/8i0q_35106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i0q_35106/04_2025/8i0q_35106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i0q_35106/04_2025/8i0q_35106.cif"
  }
  resolution = 4.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8}
          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: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 8}
          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: {'GLN:plan1': 3, 'ARG:plan': 1}
          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: {'GLN:plan1': 2, 'ARG:plan': 1}
          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: {'PHE:plan': 1, 'GLU: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: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 5.51, per 1000 atoms: 0.62
  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: 2.17
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.20
  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: 2.64

  Time building geometry restraints manager: 2.58 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:             1.270
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.130
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.120
-------------------------------------------------------------------------------
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 : 9.44
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (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
 TRP   0.003   0.001   TRP H 106 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.009   0.001   PHE L  72 
 TYR   0.008   0.001   TYR B 113 
 ARG   0.006   0.000   ARG H 101 

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

*********************** 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  : 1.034 
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: 0.1546
  time to fit residues: 10.6168
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  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    2.2386

-------------------------------------------------------------------------------
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 = 0.2982 r_free = 0.2982 target = 0.037576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.030409 restraints weight = 88704.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.031295 restraints weight = 56444.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031953 restraints weight = 41411.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9047  Z= 0.187
  Angle     :  0.649   5.457  12381  Z= 0.339
  Chirality :  0.044   0.149   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  8.020  88.274   1314
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.25), residues: 1162
  helix: -1.01 (0.99), residues: 24
  sheet: -0.99 (0.22), residues: 482
  loop : -0.54 (0.26), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  39 
 HIS   0.007   0.002   HIS B 210 
 PHE   0.017   0.002   PHE B 190 
 TYR   0.017   0.002   TYR I 107 
 ARG   0.004   0.001   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  287)
  hydrogen bonds       : angle       7.07241 (  792)
  SS BOND              : bond        0.00737 (    4)
  SS BOND              : angle       0.74945 (    8)
  covalent geometry    : bond        0.00388 ( 9043)
  covalent geometry    : angle       0.64888 (12373)

*********************** 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  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8184 (p) cc_final: 0.7701 (p)
REVERT: A  352 MET cc_start: 0.8784 (ptm) cc_final: 0.8258 (ptm)
REVERT: B  150 CYS cc_start: 0.8461 (p) cc_final: 0.7946 (p)
REVERT: H   21 LEU cc_start: 0.9469 (mt) cc_final: 0.9202 (tp)
REVERT: H   86 MET cc_start: 0.7763 (pmm) cc_final: 0.7499 (pmm)
REVERT: I   21 LEU cc_start: 0.9564 (mt) cc_final: 0.9229 (tp)
REVERT: I   86 MET cc_start: 0.7640 (pmm) cc_final: 0.7302 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1581
  time to fit residues: 9.5705
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  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
M   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.037902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.030647 restraints weight = 88288.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031564 restraints weight = 55407.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.032246 restraints weight = 40287.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9047  Z= 0.139
  Angle     :  0.578   5.185  12381  Z= 0.298
  Chirality :  0.043   0.147   1436
  Planarity :  0.004   0.031   1587
  Dihedral  :  7.728  85.517   1314
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.25), residues: 1162
  helix: -0.53 (1.03), residues: 24
  sheet: -0.79 (0.22), residues: 480
  loop : -0.43 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  39 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.014   0.002   PHE A 190 
 TYR   0.012   0.001   TYR A 249 
 ARG   0.003   0.001   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  287)
  hydrogen bonds       : angle       6.24355 (  792)
  SS BOND              : bond        0.00596 (    4)
  SS BOND              : angle       0.55642 (    8)
  covalent geometry    : bond        0.00293 ( 9043)
  covalent geometry    : angle       0.57818 (12373)

*********************** 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
  38 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8093 (p) cc_final: 0.7700 (p)
REVERT: A  352 MET cc_start: 0.8568 (ptm) cc_final: 0.7637 (ptm)
REVERT: B  150 CYS cc_start: 0.8057 (p) cc_final: 0.7609 (p)
REVERT: I   86 MET cc_start: 0.8259 (pmm) cc_final: 0.8036 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1552
  time to fit residues: 9.9949
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  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    0.0170
   chunk 60 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0470
   chunk 23 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 110 optimal weight:    9.9990
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
B 172 GLN
M  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.039625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.032036 restraints weight = 85490.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.032966 restraints weight = 55040.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.033629 restraints weight = 40339.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9047  Z= 0.087
  Angle     :  0.541   8.204  12381  Z= 0.267
  Chirality :  0.043   0.159   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  7.278  82.490   1314
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.12 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1162
  helix:  0.06 (1.05), residues: 24
  sheet: -0.34 (0.23), residues: 480
  loop : -0.35 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP M  36 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.010   0.001   PHE L  72 
 TYR   0.007   0.001   TYR I  60 
 ARG   0.003   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02641 (  287)
  hydrogen bonds       : angle       5.43343 (  792)
  SS BOND              : bond        0.00522 (    4)
  SS BOND              : angle       0.27817 (    8)
  covalent geometry    : bond        0.00190 ( 9043)
  covalent geometry    : angle       0.54141 (12373)

*********************** 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
  42 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8886 (p90) cc_final: 0.8634 (p90)
REVERT: A  150 CYS cc_start: 0.7927 (p) cc_final: 0.7293 (p)
REVERT: A  352 MET cc_start: 0.8392 (ptm) cc_final: 0.7410 (ptm)
REVERT: B  150 CYS cc_start: 0.7711 (p) cc_final: 0.7317 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1620
  time to fit residues: 11.3769
Evaluate side-chains
  30 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0000
   chunk 40 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 111 optimal weight:    0.6980
   overall best weight:    2.7390

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

Flipped N/Q/H residues before XYZ refinement:
B 172 GLN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.037238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.030288 restraints weight = 90209.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.031130 restraints weight = 58944.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.031732 restraints weight = 43517.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9047  Z= 0.215
  Angle     :  0.650   5.892  12381  Z= 0.338
  Chirality :  0.043   0.150   1436
  Planarity :  0.004   0.034   1587
  Dihedral  :  7.886  82.138   1314
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.79 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1162
  helix: -0.55 (1.01), residues: 24
  sheet: -0.77 (0.22), residues: 490
  loop : -0.49 (0.26), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H  39 
 HIS   0.008   0.002   HIS B 210 
 PHE   0.021   0.003   PHE A 190 
 TYR   0.021   0.002   TYR I 107 
 ARG   0.005   0.001   ARG I  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  287)
  hydrogen bonds       : angle       6.26454 (  792)
  SS BOND              : bond        0.00929 (    4)
  SS BOND              : angle       0.26233 (    8)
  covalent geometry    : bond        0.00444 ( 9043)
  covalent geometry    : angle       0.64983 (12373)

*********************** 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
  35 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8102 (p) cc_final: 0.7740 (p)
REVERT: A  352 MET cc_start: 0.8308 (ptm) cc_final: 0.7219 (ptm)
REVERT: B  150 CYS cc_start: 0.8024 (p) cc_final: 0.7654 (p)
REVERT: B  172 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8240 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1696
  time to fit residues: 10.1510
Evaluate side-chains
  21 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    0.1980
   chunk 102 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3011 r_free = 0.3011 target = 0.037944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.030732 restraints weight = 87803.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031664 restraints weight = 55322.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032335 restraints weight = 40023.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9047  Z= 0.137
  Angle     :  0.574   5.199  12381  Z= 0.293
  Chirality :  0.042   0.152   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  7.615  83.635   1314
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.25), residues: 1162
  helix: -0.18 (1.08), residues: 24
  sheet: -0.62 (0.23), residues: 478
  loop : -0.44 (0.26), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  39 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.013   0.002   PHE B 190 
 TYR   0.010   0.001   TYR I 107 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03086 (  287)
  hydrogen bonds       : angle       5.81851 (  792)
  SS BOND              : bond        0.00594 (    4)
  SS BOND              : angle       0.27813 (    8)
  covalent geometry    : bond        0.00294 ( 9043)
  covalent geometry    : angle       0.57433 (12373)

*********************** 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
  34 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8224 (p) cc_final: 0.7848 (p)
REVERT: A  352 MET cc_start: 0.8338 (ptm) cc_final: 0.7148 (ptm)
REVERT: B  150 CYS cc_start: 0.8094 (p) cc_final: 0.7684 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1749
  time to fit residues: 10.1285
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  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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**
** 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 = 0.3004 r_free = 0.3004 target = 0.037929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.030683 restraints weight = 89185.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031590 restraints weight = 56870.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032249 restraints weight = 41486.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9047  Z= 0.146
  Angle     :  0.580   5.641  12381  Z= 0.296
  Chirality :  0.042   0.149   1436
  Planarity :  0.004   0.033   1587
  Dihedral  :  7.584  84.150   1314
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.25), residues: 1162
  helix: -0.25 (1.06), residues: 24
  sheet: -0.63 (0.23), residues: 474
  loop : -0.43 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  39 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.039   0.002   PHE H 105 
 TYR   0.012   0.001   TYR I 107 
 ARG   0.004   0.000   ARG H 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  287)
  hydrogen bonds       : angle       5.76048 (  792)
  SS BOND              : bond        0.00607 (    4)
  SS BOND              : angle       0.25593 (    8)
  covalent geometry    : bond        0.00309 ( 9043)
  covalent geometry    : angle       0.58056 (12373)

*********************** 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
  32 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A  150 CYS cc_start: 0.8111 (p) cc_final: 0.7751 (p)
REVERT: A  352 MET cc_start: 0.8255 (ptm) cc_final: 0.7094 (ptm)
REVERT: B  150 CYS cc_start: 0.8012 (p) cc_final: 0.7622 (p)
REVERT: B  352 MET cc_start: 0.8424 (ttt) cc_final: 0.7990 (ttt)
REVERT: L   24 CYS cc_start: 0.1878 (t) cc_final: 0.1134 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1565
  time to fit residues: 9.4242
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  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 84 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 106 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.9386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.039069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.031595 restraints weight = 87558.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032519 restraints weight = 56462.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.033192 restraints weight = 41335.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9047  Z= 0.100
  Angle     :  0.553  10.600  12381  Z= 0.275
  Chirality :  0.042   0.151   1436
  Planarity :  0.003   0.027   1587
  Dihedral  :  7.345  85.012   1314
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.25), residues: 1162
  helix:  0.29 (1.09), residues: 24
  sheet: -0.43 (0.23), residues: 480
  loop : -0.36 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP I  39 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.038   0.002   PHE I 105 
 TYR   0.007   0.001   TYR A 249 
 ARG   0.008   0.001   ARG I 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02697 (  287)
  hydrogen bonds       : angle       5.33982 (  792)
  SS BOND              : bond        0.00510 (    4)
  SS BOND              : angle       0.68914 (    8)
  covalent geometry    : bond        0.00221 ( 9043)
  covalent geometry    : angle       0.55330 (12373)

*********************** 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
  35 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  150 CYS cc_start: 0.7981 (p) cc_final: 0.7587 (p)
REVERT: A  352 MET cc_start: 0.8459 (ptm) cc_final: 0.7452 (ptm)
REVERT: B  150 CYS cc_start: 0.7807 (p) cc_final: 0.7377 (p)
REVERT: B  352 MET cc_start: 0.8458 (ttt) cc_final: 0.7903 (ttt)
REVERT: H   21 LEU cc_start: 0.9402 (pt) cc_final: 0.9182 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1458
  time to fit residues: 8.9886
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  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 112 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**
M   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.038465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.031149 restraints weight = 91896.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.032085 restraints weight = 58185.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.032745 restraints weight = 42280.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9047  Z= 0.119
  Angle     :  0.548   5.004  12381  Z= 0.276
  Chirality :  0.042   0.147   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  7.308  84.864   1314
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1162
  helix:  0.37 (1.07), residues: 24
  sheet: -0.41 (0.23), residues: 480
  loop : -0.36 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  39 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.029   0.002   PHE I 105 
 TYR   0.012   0.001   TYR H 107 
 ARG   0.002   0.000   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02797 (  287)
  hydrogen bonds       : angle       5.33330 (  792)
  SS BOND              : bond        0.00532 (    4)
  SS BOND              : angle       0.24953 (    8)
  covalent geometry    : bond        0.00256 ( 9043)
  covalent geometry    : angle       0.54772 (12373)

*********************** 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
  34 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8071 (p) cc_final: 0.7677 (p)
REVERT: A  352 MET cc_start: 0.8501 (ptm) cc_final: 0.7503 (ptm)
REVERT: B  150 CYS cc_start: 0.7884 (p) cc_final: 0.7437 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1530
  time to fit residues: 8.9779
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  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0270
   chunk 17 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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**
M   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.039551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.032059 restraints weight = 89351.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.033009 restraints weight = 57025.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.033682 restraints weight = 41590.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9047  Z= 0.084
  Angle     :  0.526   5.172  12381  Z= 0.258
  Chirality :  0.042   0.149   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  7.040  85.603   1314
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.25), residues: 1162
  helix:  0.80 (1.07), residues: 24
  sheet: -0.19 (0.23), residues: 480
  loop : -0.32 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP M  36 
 HIS   0.003   0.001   HIS B 210 
 PHE   0.026   0.001   PHE I 105 
 TYR   0.007   0.001   TYR A 113 
 ARG   0.002   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02428 (  287)
  hydrogen bonds       : angle       4.92913 (  792)
  SS BOND              : bond        0.00465 (    4)
  SS BOND              : angle       0.28234 (    8)
  covalent geometry    : bond        0.00188 ( 9043)
  covalent geometry    : angle       0.52564 (12373)

********************** 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
  41 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.9133 (p90) cc_final: 0.8755 (p90)
REVERT: A  150 CYS cc_start: 0.7895 (p) cc_final: 0.7287 (p)
REVERT: A  352 MET cc_start: 0.8606 (ptm) cc_final: 0.7532 (ptm)
REVERT: B  150 CYS cc_start: 0.7797 (p) cc_final: 0.7413 (p)
REVERT: H   21 LEU cc_start: 0.9321 (pt) cc_final: 0.9075 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1487
  time to fit residues: 10.3936
Evaluate side-chains
  28 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0770
   chunk 109 optimal weight:    7.9990
   overall best weight:    1.6146

-------------------------------------------------------------------------------
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 = 0.3016 r_free = 0.3016 target = 0.038416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.031161 restraints weight = 92975.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.032073 restraints weight = 58954.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.032726 restraints weight = 42939.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9047  Z= 0.137
  Angle     :  0.557   5.017  12381  Z= 0.282
  Chirality :  0.042   0.143   1436
  Planarity :  0.004   0.029   1587
  Dihedral  :  7.203  84.357   1314
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1162
  helix:  0.65 (1.06), residues: 24
  sheet: -0.35 (0.23), residues: 476
  loop : -0.42 (0.26), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  39 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.024   0.002   PHE I 105 
 TYR   0.013   0.001   TYR H 107 
 ARG   0.003   0.000   ARG I  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02911 (  287)
  hydrogen bonds       : angle       5.19970 (  792)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       0.29144 (    8)
  covalent geometry    : bond        0.00290 ( 9043)
  covalent geometry    : angle       0.55715 (12373)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2493.81 seconds
wall clock time: 44 minutes 43.48 seconds (2683.48 seconds total)