Starting phenix.real_space_refine
on Thu Mar 13 15:13:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i0q_35106/03_2025/8i0q_35106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i0q_35106/03_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_35106/03_2025/8i0q_35106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i0q_35106/03_2025/8i0q_35106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i0q_35106/03_2025/8i0q_35106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i0q_35106/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.58, per 1000 atoms: 0.63
  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: 2.26
  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: 1.30
  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: 2.47

  Time building geometry restraints manager: 2.67 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:             0.700
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.170
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.340
-------------------------------------------------------------------------------
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   9043  Z= 0.204
  Angle     :  0.593   8.393  12373  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 

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

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.933 
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: 0.1488
  time to fit residues: 10.1949
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  : 0.950 
-------------------------------------------------------------------------------
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:    0.9990
   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:    2.2588

-------------------------------------------------------------------------------
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 = 0.2980 r_free = 0.2980 target = 0.037505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.030342 restraints weight = 88834.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.031257 restraints weight = 56442.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.031905 restraints weight = 40985.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9043  Z= 0.256
  Angle     :  0.651   5.545  12373  Z= 0.340
  Chirality :  0.044   0.151   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  8.050  88.905   1314
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  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: -0.99 (1.00), residues: 24
  sheet: -0.99 (0.22), residues: 482
  loop : -0.55 (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   0.018   0.003   PHE B 190 
 TYR   0.019   0.002   TYR I 107 
 ARG   0.005   0.001   ARG M  62 

*********************** 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  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8178 (p) cc_final: 0.7704 (p)
REVERT: A  352 MET cc_start: 0.8871 (ptm) cc_final: 0.7901 (ptm)
REVERT: B  150 CYS cc_start: 0.8457 (p) cc_final: 0.7942 (p)
REVERT: H   21 LEU cc_start: 0.9468 (mt) cc_final: 0.9201 (tp)
REVERT: H   86 MET cc_start: 0.7764 (pmm) cc_final: 0.7499 (pmm)
REVERT: I   21 LEU cc_start: 0.9561 (mt) cc_final: 0.9225 (tp)
REVERT: I   86 MET cc_start: 0.7756 (pmm) cc_final: 0.7474 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1590
  time to fit residues: 9.6988
Evaluate side-chains
  27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0070
   chunk 53 optimal weight:    0.2980
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.0202

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.038737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.031363 restraints weight = 88873.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.032321 restraints weight = 55870.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033006 restraints weight = 40319.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9043  Z= 0.146
  Angle     :  0.558   5.092  12373  Z= 0.285
  Chirality :  0.043   0.149   1436
  Planarity :  0.004   0.031   1587
  Dihedral  :  7.599  87.261   1314
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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: -0.93 (0.25), residues: 1162
  helix: -0.27 (1.07), residues: 24
  sheet: -0.63 (0.22), residues: 494
  loop : -0.51 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  39 
 HIS   0.004   0.001   HIS B 353 
 PHE   0.011   0.002   PHE L  72 
 TYR   0.010   0.001   TYR A 249 
 ARG   0.006   0.000   ARG H  70 

*********************** 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
  43 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.7929 (p) cc_final: 0.7523 (p)
REVERT: A  352 MET cc_start: 0.8761 (ptm) cc_final: 0.7754 (ptm)
REVERT: B  150 CYS cc_start: 0.7854 (p) cc_final: 0.7344 (p)
REVERT: B  352 MET cc_start: 0.9007 (ttt) cc_final: 0.8761 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1761
  time to fit residues: 12.4228
Evaluate side-chains
  28 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 60 optimal weight:    5.9990
   chunk 96 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    1.7000

-------------------------------------------------------------------------------
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   4 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.037990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.030873 restraints weight = 90390.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.031743 restraints weight = 58585.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.032375 restraints weight = 43219.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9043  Z= 0.202
  Angle     :  0.578   7.333  12373  Z= 0.295
  Chirality :  0.042   0.156   1436
  Planarity :  0.004   0.033   1587
  Dihedral  :  7.603  81.031   1314
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  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: -0.16 (1.07), residues: 24
  sheet: -0.61 (0.23), residues: 488
  loop : -0.44 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  39 
 HIS   0.006   0.002   HIS B 210 
 PHE   0.015   0.002   PHE B 190 
 TYR   0.014   0.001   TYR I 107 
 ARG   0.003   0.000   ARG I  90 

*********************** 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
  39 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.7969 (p) cc_final: 0.7562 (p)
REVERT: A  352 MET cc_start: 0.8344 (ptm) cc_final: 0.7485 (ptm)
REVERT: B  150 CYS cc_start: 0.7691 (p) cc_final: 0.7216 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1714
  time to fit residues: 11.1922
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  : 1.073 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 111 optimal weight:    0.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3000 r_free = 0.3000 target = 0.037713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.030521 restraints weight = 88520.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.031445 restraints weight = 56017.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.032112 restraints weight = 40737.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9043  Z= 0.223
  Angle     :  0.591   5.208  12373  Z= 0.303
  Chirality :  0.042   0.154   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  7.697  82.439   1314
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.91 (0.25), residues: 1162
  helix: -0.32 (1.04), residues: 24
  sheet: -0.69 (0.23), residues: 480
  loop : -0.44 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  39 
 HIS   0.006   0.002   HIS B 210 
 PHE   0.016   0.002   PHE A 190 
 TYR   0.013   0.001   TYR I 107 
 ARG   0.003   0.000   ARG I  90 

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

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8230 (p) cc_final: 0.7824 (p)
REVERT: A  352 MET cc_start: 0.8339 (ptm) cc_final: 0.7295 (ptm)
REVERT: B  150 CYS cc_start: 0.8137 (p) cc_final: 0.7717 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1472
  time to fit residues: 9.2908
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  : 0.909 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   chunk 69 optimal weight:    9.9990
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.038344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.031021 restraints weight = 87130.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.031957 restraints weight = 55522.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.032629 restraints weight = 40489.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9043  Z= 0.171
  Angle     :  0.552   5.118  12373  Z= 0.279
  Chirality :  0.042   0.151   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  7.454  83.727   1314
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.25), residues: 1162
  helix:  0.07 (1.11), residues: 24
  sheet: -0.54 (0.23), residues: 484
  loop : -0.43 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  39 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.013   0.002   PHE B 190 
 TYR   0.009   0.001   TYR A 249 
 ARG   0.002   0.000   ARG I  90 

*********************** 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
  36 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.024 
Fit side-chains
REVERT: A  150 CYS cc_start: 0.8179 (p) cc_final: 0.7855 (p)
REVERT: A  352 MET cc_start: 0.8231 (ptm) cc_final: 0.7174 (ptm)
REVERT: B  150 CYS cc_start: 0.8018 (p) cc_final: 0.7554 (p)
REVERT: B  352 MET cc_start: 0.8472 (ttt) cc_final: 0.8212 (ttt)
REVERT: L   24 CYS cc_start: 0.2102 (t) cc_final: 0.1424 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1714
  time to fit residues: 10.2546
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  : 1.012 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 89 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 67 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.039006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.031498 restraints weight = 86010.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032429 restraints weight = 55203.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.033107 restraints weight = 40318.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9043  Z= 0.153
  Angle     :  0.549   9.651  12373  Z= 0.274
  Chirality :  0.042   0.152   1436
  Planarity :  0.004   0.032   1587
  Dihedral  :  7.324  84.245   1314
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  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: -0.67 (0.25), residues: 1162
  helix:  0.34 (1.09), residues: 24
  sheet: -0.42 (0.23), residues: 480
  loop : -0.40 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  39 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.043   0.002   PHE H 105 
 TYR   0.008   0.001   TYR A 113 
 ARG   0.004   0.000   ARG M  62 

*********************** 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
  37 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 CYS cc_start: 0.8021 (p) cc_final: 0.7625 (p)
REVERT: A  352 MET cc_start: 0.8134 (ptm) cc_final: 0.7125 (ptm)
REVERT: B  150 CYS cc_start: 0.7816 (p) cc_final: 0.7425 (p)
REVERT: L   24 CYS cc_start: 0.1703 (t) cc_final: 0.1499 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1725
  time to fit residues: 10.5755
Evaluate side-chains
  23 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 35 optimal weight:    0.3980
   chunk 107 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 84 optimal weight:    0.0270
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.040108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.032338 restraints weight = 85338.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.033298 restraints weight = 55177.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.033981 restraints weight = 40525.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9043  Z= 0.120
  Angle     :  0.527   5.145  12373  Z= 0.257
  Chirality :  0.042   0.151   1436
  Planarity :  0.003   0.028   1587
  Dihedral  :  6.993  85.426   1314
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.67 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.36 (0.25), residues: 1162
  helix:  0.86 (1.05), residues: 24
  sheet: -0.08 (0.23), residues: 480
  loop : -0.31 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP M  36 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.032   0.001   PHE I 105 
 TYR   0.006   0.001   TYR B 113 
 ARG   0.008   0.000   ARG L  62 

*********************** 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
  47 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  149 PHE cc_start: 0.9106 (p90) cc_final: 0.8824 (p90)
REVERT: A  352 MET cc_start: 0.8665 (ptm) cc_final: 0.8279 (ptm)
REVERT: B  352 MET cc_start: 0.8495 (ttt) cc_final: 0.8285 (ttt)
REVERT: H   21 LEU cc_start: 0.9303 (pt) cc_final: 0.9089 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1794
  time to fit residues: 13.4323
Evaluate side-chains
  27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 47 optimal weight:    0.2980
   chunk 25 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0000
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.039270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031667 restraints weight = 87416.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.032591 restraints weight = 56359.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.033262 restraints weight = 41393.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9043  Z= 0.147
  Angle     :  0.527   5.012  12373  Z= 0.263
  Chirality :  0.041   0.146   1436
  Planarity :  0.004   0.030   1587
  Dihedral  :  6.986  84.301   1314
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.40 (0.25), residues: 1162
  helix:  1.07 (1.09), residues: 24
  sheet: -0.08 (0.23), residues: 476
  loop : -0.37 (0.25), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  39 
 HIS   0.003   0.001   HIS B 210 
 PHE   0.029   0.002   PHE I 105 
 TYR   0.008   0.001   TYR I 107 
 ARG   0.003   0.000   ARG L  62 

*********************** 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
  40 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A  149 PHE cc_start: 0.9065 (p90) cc_final: 0.8803 (p90)
REVERT: A  150 CYS cc_start: 0.7891 (p) cc_final: 0.7346 (p)
REVERT: A  352 MET cc_start: 0.8422 (ptm) cc_final: 0.7229 (ptm)
REVERT: B  150 CYS cc_start: 0.7796 (p) cc_final: 0.7476 (p)
REVERT: B  352 MET cc_start: 0.8480 (ttt) cc_final: 0.7935 (ttt)
REVERT: H   84 LEU cc_start: 0.8852 (mm) cc_final: 0.8637 (mt)
REVERT: I   84 LEU cc_start: 0.8692 (mm) cc_final: 0.8483 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1645
  time to fit residues: 10.8346
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  : 1.037 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 172 GLN
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.039460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.031850 restraints weight = 87092.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.032788 restraints weight = 55639.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.033465 restraints weight = 40607.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9043  Z= 0.137
  Angle     :  0.519   5.058  12373  Z= 0.257
  Chirality :  0.041   0.144   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  6.941  84.533   1314
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    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: -0.31 (0.25), residues: 1162
  helix:  1.16 (1.11), residues: 24
  sheet:  0.05 (0.24), residues: 468
  loop : -0.38 (0.25), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M  36 
 HIS   0.004   0.001   HIS B 210 
 PHE   0.025   0.002   PHE I 105 
 TYR   0.007   0.001   TYR A 113 
 ARG   0.002   0.000   ARG I  90 

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

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A  149 PHE cc_start: 0.9084 (p90) cc_final: 0.8813 (p90)
REVERT: A  150 CYS cc_start: 0.7941 (p) cc_final: 0.7396 (p)
REVERT: A  352 MET cc_start: 0.8449 (ptm) cc_final: 0.7233 (ptm)
REVERT: B  150 CYS cc_start: 0.7762 (p) cc_final: 0.7409 (p)
REVERT: B  352 MET cc_start: 0.8620 (ttt) cc_final: 0.8273 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1773
  time to fit residues: 12.3785
Evaluate side-chains
  27 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0470
   chunk 92 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0470
   chunk 107 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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 172 GLN
** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.040252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.032668 restraints weight = 87431.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.033605 restraints weight = 56055.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.034297 restraints weight = 40952.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9043  Z= 0.113
  Angle     :  0.505   5.425  12373  Z= 0.246
  Chirality :  0.041   0.145   1436
  Planarity :  0.003   0.029   1587
  Dihedral  :  6.750  85.212   1314
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -0.12 (0.25), residues: 1162
  helix:  1.19 (1.09), residues: 24
  sheet:  0.28 (0.24), residues: 482
  loop : -0.35 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP M  36 
 HIS   0.002   0.001   HIS B 210 
 PHE   0.024   0.001   PHE I 105 
 TYR   0.008   0.001   TYR B 173 
 ARG   0.002   0.000   ARG I  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2397.05 seconds
wall clock time: 43 minutes 11.57 seconds (2591.57 seconds total)