Starting phenix.real_space_refine
on Fri Mar 15 21:44:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tup_41628/03_2024/8tup_41628.pdb"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
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
     Mg      3      5.21       5
     S      65      5.16       5
     C    8210      2.51       5
     N    2155      2.21       5
     O    2436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  101": "OE1" <-> "OE2"
    Residue "A PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  101": "OE1" <-> "OE2"
    Residue "B PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  101": "OE1" <-> "OE2"
    Residue "C PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  101": "OE1" <-> "OE2"
    Residue "D PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  101": "OE1" <-> "OE2"
    Residue "E PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 12869
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2560
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2560
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2560
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2560
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2560
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "D"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "E"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 6.63, per 1000 atoms: 0.52
  Number of scatterers: 12869
  At special positions: 0
  Unit cell: (107.07, 108.73, 140.27, 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      65     16.00
     Mg      3     11.99
     O    2436      8.00
     N    2155      7.00
     C    8210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 4.95
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3030

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 5 sheets defined
      69.5% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.953A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   PHE A 120 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 120'
    Processing helix  chain 'A' and resid 161 through 166
    Processing helix  chain 'A' and resid 166 through 172
    Processing helix  chain 'A' and resid 183 through 219
      Proline residue:  A 209  - end of helix
      removed outlier: 3.755A  pdb=" N   ALA A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 218 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 3.606A  pdb=" N   LEU A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   HIS A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 268
      removed outlier: 3.528A  pdb=" N   LEU A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.168A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 360
      removed outlier: 3.772A  pdb=" N   MET A 292 " --> pdb=" O   HIS A 288 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ARG A 332 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 399
      removed outlier: 3.610A  pdb=" N   GLY A 386 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.954A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   PHE B 120 " --> pdb=" O   ASP B 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 116 through 120'
    Processing helix  chain 'B' and resid 161 through 166
    Processing helix  chain 'B' and resid 166 through 172
    Processing helix  chain 'B' and resid 183 through 219
      Proline residue:  B 209  - end of helix
      removed outlier: 3.755A  pdb=" N   ALA B 217 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 218 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 3.605A  pdb=" N   LEU B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   HIS B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 268
      removed outlier: 3.528A  pdb=" N   LEU B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 4.168A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 360
      removed outlier: 3.772A  pdb=" N   MET B 292 " --> pdb=" O   HIS B 288 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP B 329 " --> pdb=" O   PHE B 325 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ARG B 332 " --> pdb=" O   LEU B 328 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET B 335 " --> pdb=" O   HIS B 331 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   MET B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLY B 356 " --> pdb=" O   PHE B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 399
      removed outlier: 3.611A  pdb=" N   GLY B 386 " --> pdb=" O   PHE B 382 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 116 through 120
      removed outlier: 3.954A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   PHE C 120 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 116 through 120'
    Processing helix  chain 'C' and resid 161 through 166
    Processing helix  chain 'C' and resid 166 through 172
    Processing helix  chain 'C' and resid 183 through 219
      Proline residue:  C 209  - end of helix
      removed outlier: 3.754A  pdb=" N   ALA C 217 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C 218 " --> pdb=" O   THR C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 3.606A  pdb=" N   LEU C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   HIS C 232 " --> pdb=" O   ARG C 228 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE C 233 " --> pdb=" O   SER C 229 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 268
      removed outlier: 3.528A  pdb=" N   LEU C 268 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
    Processing helix  chain 'C' and resid 277 through 282
      removed outlier: 4.168A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 360
      removed outlier: 3.772A  pdb=" N   MET C 292 " --> pdb=" O   HIS C 288 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP C 329 " --> pdb=" O   PHE C 325 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ARG C 332 " --> pdb=" O   LEU C 328 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL C 334 " --> pdb=" O   SER C 330 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET C 335 " --> pdb=" O   HIS C 331 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET C 355 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLY C 356 " --> pdb=" O   PHE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 399
      removed outlier: 3.610A  pdb=" N   GLY C 386 " --> pdb=" O   PHE C 382 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU C 396 " --> pdb=" O   LEU C 392 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY C 397 " --> pdb=" O   LEU C 393 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 116 through 120
      removed outlier: 3.953A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   PHE D 120 " --> pdb=" O   ASP D 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 116 through 120'
    Processing helix  chain 'D' and resid 161 through 166
    Processing helix  chain 'D' and resid 166 through 172
    Processing helix  chain 'D' and resid 183 through 219
      Proline residue:  D 209  - end of helix
      removed outlier: 3.755A  pdb=" N   ALA D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 3.606A  pdb=" N   LEU D 231 " --> pdb=" O   ASP D 227 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   HIS D 232 " --> pdb=" O   ARG D 228 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE D 233 " --> pdb=" O   SER D 229 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 268
      removed outlier: 3.529A  pdb=" N   LEU D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
    Processing helix  chain 'D' and resid 277 through 282
      removed outlier: 4.168A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 360
      removed outlier: 3.772A  pdb=" N   MET D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP D 329 " --> pdb=" O   PHE D 325 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ARG D 332 " --> pdb=" O   LEU D 328 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL D 334 " --> pdb=" O   SER D 330 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET D 335 " --> pdb=" O   HIS D 331 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY D 356 " --> pdb=" O   PHE D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 399
      removed outlier: 3.610A  pdb=" N   GLY D 386 " --> pdb=" O   PHE D 382 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU D 396 " --> pdb=" O   LEU D 392 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY D 397 " --> pdb=" O   LEU D 393 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 116 through 120
      removed outlier: 3.953A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   PHE E 120 " --> pdb=" O   ASP E 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 116 through 120'
    Processing helix  chain 'E' and resid 161 through 166
    Processing helix  chain 'E' and resid 166 through 172
    Processing helix  chain 'E' and resid 183 through 219
      Proline residue:  E 209  - end of helix
      removed outlier: 3.755A  pdb=" N   ALA E 217 " --> pdb=" O   GLU E 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU E 218 " --> pdb=" O   THR E 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 3.605A  pdb=" N   LEU E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   HIS E 232 " --> pdb=" O   ARG E 228 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE E 233 " --> pdb=" O   SER E 229 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE E 258 " --> pdb=" O   SER E 254 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 268
      removed outlier: 3.528A  pdb=" N   LEU E 268 " --> pdb=" O   LEU E 264 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
    Processing helix  chain 'E' and resid 277 through 282
      removed outlier: 4.167A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 360
      removed outlier: 3.772A  pdb=" N   MET E 292 " --> pdb=" O   HIS E 288 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP E 329 " --> pdb=" O   PHE E 325 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ARG E 332 " --> pdb=" O   LEU E 328 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL E 334 " --> pdb=" O   SER E 330 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET E 335 " --> pdb=" O   HIS E 331 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY E 356 " --> pdb=" O   PHE E 352 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 372 through 399
      removed outlier: 3.611A  pdb=" N   GLY E 386 " --> pdb=" O   PHE E 382 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU E 396 " --> pdb=" O   LEU E 392 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY E 397 " --> pdb=" O   LEU E 393 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 3.803A  pdb=" N   VAL A  88 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 102 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103
      removed outlier: 3.803A  pdb=" N   VAL B  88 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG B 102 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103
      removed outlier: 3.803A  pdb=" N   VAL C  88 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG C 102 " --> pdb=" O   PHE C  86 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103
      removed outlier: 3.803A  pdb=" N   VAL D  88 " --> pdb=" O   PHE D 100 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG D 102 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103
      removed outlier: 3.803A  pdb=" N   VAL E  88 " --> pdb=" O   PHE E 100 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG E 102 " --> pdb=" O   PHE E  86 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    885 hydrogen bonds defined for protein.
    2625 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: 3.65

  Time building geometry restraints manager: 5.35 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: 4230
        1.34 -     1.46: 2607
        1.46 -     1.58: 6068
        1.58 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13025
  Sorted by residual:
  bond pdb=" CB  PRO A 221 "
       pdb=" CG  PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.533 -0.041 5.00e-02 4.00e+02 6.67e-01
  bond pdb=" CB  PRO D 221 "
       pdb=" CG  PRO D 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.55e-01
  bond pdb=" CB  PRO E 221 "
       pdb=" CG  PRO E 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.50e-01
  bond pdb=" CB  PRO C 221 "
       pdb=" CG  PRO C 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.46e-01
  bond pdb=" CB  PRO B 221 "
       pdb=" CG  PRO B 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.33e-01
  ... (remaining 13020 not shown)

  Histogram of bond angle deviations from ideal:
       98.35 -   105.49: 180
      105.49 -   112.63: 6933
      112.63 -   119.76: 4341
      119.76 -   126.90: 6010
      126.90 -   134.04: 131
  Bond angle restraints: 17595
  Sorted by residual:
  angle pdb=" CA  GLU D 101 "
        pdb=" CB  GLU D 101 "
        pdb=" CG  GLU D 101 "
      ideal   model   delta    sigma   weight residual
     114.10  118.23   -4.13 2.00e+00 2.50e-01 4.27e+00
  angle pdb=" CA  GLU B 101 "
        pdb=" CB  GLU B 101 "
        pdb=" CG  GLU B 101 "
      ideal   model   delta    sigma   weight residual
     114.10  118.23   -4.13 2.00e+00 2.50e-01 4.26e+00
  angle pdb=" CA  GLU C 101 "
        pdb=" CB  GLU C 101 "
        pdb=" CG  GLU C 101 "
      ideal   model   delta    sigma   weight residual
     114.10  118.23   -4.13 2.00e+00 2.50e-01 4.26e+00
  angle pdb=" CA  GLU A 101 "
        pdb=" CB  GLU A 101 "
        pdb=" CG  GLU A 101 "
      ideal   model   delta    sigma   weight residual
     114.10  118.19   -4.09 2.00e+00 2.50e-01 4.18e+00
  angle pdb=" CA  GLU E 101 "
        pdb=" CB  GLU E 101 "
        pdb=" CG  GLU E 101 "
      ideal   model   delta    sigma   weight residual
     114.10  118.18   -4.08 2.00e+00 2.50e-01 4.17e+00
  ... (remaining 17590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.14: 6905
       16.14 -    32.27: 721
       32.27 -    48.41: 229
       48.41 -    64.54: 50
       64.54 -    80.68: 10
  Dihedral angle restraints: 7915
    sinusoidal: 3270
      harmonic: 4645
  Sorted by residual:
  dihedral pdb=" CB  MET D 381 "
           pdb=" CG  MET D 381 "
           pdb=" SD  MET D 381 "
           pdb=" CE  MET D 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    2.99   57.01     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CB  MET C 381 "
           pdb=" CG  MET C 381 "
           pdb=" SD  MET C 381 "
           pdb=" CE  MET C 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    3.00   57.00     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CB  MET E 381 "
           pdb=" CG  MET E 381 "
           pdb=" SD  MET E 381 "
           pdb=" CE  MET E 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    3.01   56.99     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 7912 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1224
       0.026 -    0.052: 545
       0.052 -    0.078: 150
       0.078 -    0.104: 77
       0.104 -    0.130: 29
  Chirality restraints: 2025
  Sorted by residual:
  chirality pdb=" CA  ILE A 126 "
            pdb=" N   ILE A 126 "
            pdb=" C   ILE A 126 "
            pdb=" CB  ILE A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE C 126 "
            pdb=" N   ILE C 126 "
            pdb=" C   ILE C 126 "
            pdb=" CB  ILE C 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE E 126 "
            pdb=" N   ILE E 126 "
            pdb=" C   ILE E 126 "
            pdb=" CB  ILE E 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 2022 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 145 "   -0.036 5.00e-02 4.00e+02   5.44e-02 4.74e+00
        pdb=" N   PRO B 146 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 145 "    0.036 5.00e-02 4.00e+02   5.44e-02 4.73e+00
        pdb=" N   PRO D 146 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 145 "   -0.036 5.00e-02 4.00e+02   5.42e-02 4.70e+00
        pdb=" N   PRO C 146 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO C 146 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 146 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3065
        2.80 -     3.33: 12153
        3.33 -     3.85: 21004
        3.85 -     4.38: 24334
        4.38 -     4.90: 43627
  Nonbonded interactions: 104183
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 125 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.277 2.440
  nonbonded pdb=" OG  SER E 125 "
            pdb=" O   HOH E 501 "
     model   vdw
     2.278 2.440
  nonbonded pdb=" OG  SER C 125 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.278 2.440
  nonbonded pdb=" OG  SER B 125 "
            pdb=" O   HOH B 601 "
     model   vdw
     2.278 2.440
  nonbonded pdb=" OG  SER A 125 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.278 2.440
  ... (remaining 104178 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 83 through 400)
  selection = (chain 'B' and resid 83 through 400)
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  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:             0.020
  Extract box with map and model:          7.140
  Check model and map are aligned:         0.180
  Set scattering table:                    0.100
  Process input model:                     34.790
  Find NCS groups from input model:        0.890
  Set up NCS constraints:                  0.060
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
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      :  0.002   0.041  13025  Z= 0.129
  Angle     :  0.406   5.513  17595  Z= 0.235
  Chirality :  0.036   0.130   2025
  Planarity :  0.003   0.054   2240
  Dihedral  : 14.814  80.680   4885
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.66 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.22), residues: 1580
  helix:  2.00 (0.16), residues: 1025
  sheet:  1.87 (0.43), residues: 135
  loop : -0.50 (0.36), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 196 
 HIS   0.003   0.001   HIS C 288 
 PHE   0.012   0.001   PHE A 352 
 TYR   0.006   0.001   TYR C 299 
 ARG   0.003   0.000   ARG B 228 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.626 
Fit side-chains
REVERT: A  336 MET cc_start: 0.8142 (mmt) cc_final: 0.7517 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2340
  time to fit residues: 26.4055
Evaluate side-chains
  70 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0470
   chunk 62 optimal weight:    5.9990
   chunk 121 optimal weight:   30.0000
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN
B 339 ASN
** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 ASN
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 339 ASN
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 339 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13025  Z= 0.233
  Angle     :  0.479   5.848  17595  Z= 0.254
  Chirality :  0.039   0.141   2025
  Planarity :  0.003   0.034   2240
  Dihedral  :  3.394  14.119   1710
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.16 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.22), residues: 1580
  helix:  2.11 (0.16), residues: 1030
  sheet:  2.02 (0.42), residues: 145
  loop : -0.04 (0.39), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.014   0.002   PHE A 352 
 TYR   0.017   0.001   TYR A 299 
 ARG   0.002   0.000   ARG C 228 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 1.809 
Fit side-chains
REVERT: B  292 MET cc_start: 0.7053 (mtt) cc_final: 0.6695 (mtt)
  outliers start: 22
  outliers final: 10
  residues processed: 105
  average time/residue: 0.3258
  time to fit residues: 50.7006
Evaluate side-chains
  83 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  206 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   chunk 95 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 141 optimal weight:    0.3980
   chunk 152 optimal weight:   20.0000
   chunk 125 optimal weight:    8.9990
   chunk 139 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 113 optimal weight:   10.0000
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13025  Z= 0.274
  Angle     :  0.504   6.374  17595  Z= 0.263
  Chirality :  0.040   0.143   2025
  Planarity :  0.003   0.037   2240
  Dihedral  :  3.544  12.762   1710
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.02 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.22), residues: 1580
  helix:  2.00 (0.15), residues: 1030
  sheet:  1.52 (0.45), residues: 135
  loop :  0.13 (0.38), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.016   0.002   PHE C 352 
 TYR   0.018   0.002   TYR E 299 
 ARG   0.005   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 1.209 
Fit side-chains
  outliers start: 31
  outliers final: 21
  residues processed: 111
  average time/residue: 0.2281
  time to fit residues: 38.2515
Evaluate side-chains
  96 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  274 SER
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  136 ARG
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  274 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 139 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0270
   chunk 141 optimal weight:    0.3980
   chunk 149 optimal weight:    0.5980
   chunk 134 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    1.0040

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13025  Z= 0.219
  Angle     :  0.468   6.595  17595  Z= 0.244
  Chirality :  0.039   0.140   2025
  Planarity :  0.003   0.037   2240
  Dihedral  :  3.426  12.776   1710
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.88 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.22), residues: 1580
  helix:  2.15 (0.15), residues: 1030
  sheet:  1.45 (0.46), residues: 135
  loop :  0.10 (0.38), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.014   0.001   PHE B 352 
 TYR   0.015   0.001   TYR E 299 
 ARG   0.004   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.509 
Fit side-chains
REVERT: B  336 MET cc_start: 0.8152 (mmt) cc_final: 0.7639 (mmt)
REVERT: C  336 MET cc_start: 0.7905 (mmt) cc_final: 0.7347 (mtp)
REVERT: E  336 MET cc_start: 0.7685 (mmt) cc_final: 0.6960 (mtt)
  outliers start: 24
  outliers final: 19
  residues processed: 101
  average time/residue: 0.2237
  time to fit residues: 35.6516
Evaluate side-chains
  97 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  265 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 127 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 134 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13025  Z= 0.168
  Angle     :  0.442   7.196  17595  Z= 0.229
  Chirality :  0.037   0.137   2025
  Planarity :  0.003   0.036   2240
  Dihedral  :  3.289  12.506   1710
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.52 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.22), residues: 1580
  helix:  2.39 (0.15), residues: 1030
  sheet:  1.42 (0.45), residues: 135
  loop :  0.07 (0.37), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.012   0.001   PHE C 352 
 TYR   0.012   0.001   TYR E 299 
 ARG   0.004   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 1.436 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8611 (tpt) cc_final: 0.8139 (tpt)
REVERT: B  292 MET cc_start: 0.7069 (mtt) cc_final: 0.6824 (mtt)
REVERT: C  336 MET cc_start: 0.7792 (mmt) cc_final: 0.7572 (mtp)
  outliers start: 32
  outliers final: 24
  residues processed: 115
  average time/residue: 0.2147
  time to fit residues: 38.9791
Evaluate side-chains
  106 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  265 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 78 optimal weight:    0.2980
   chunk 144 optimal weight:    6.9990
   overall best weight:    1.0386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13025  Z= 0.227
  Angle     :  0.493   7.503  17595  Z= 0.253
  Chirality :  0.039   0.142   2025
  Planarity :  0.003   0.036   2240
  Dihedral  :  3.422  13.814   1710
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.52 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.22), residues: 1580
  helix:  2.28 (0.15), residues: 1030
  sheet:  1.71 (0.44), residues: 145
  loop :  0.12 (0.38), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.017   0.001   TYR A 299 
 ARG   0.003   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 1.420 
Fit side-chains
REVERT: B  292 MET cc_start: 0.7179 (mtt) cc_final: 0.6859 (mtt)
  outliers start: 36
  outliers final: 33
  residues processed: 109
  average time/residue: 0.2093
  time to fit residues: 36.1501
Evaluate side-chains
  109 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  274 SER
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  274 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 85 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 149 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0870
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.5360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13025  Z= 0.150
  Angle     :  0.441   7.002  17595  Z= 0.227
  Chirality :  0.037   0.135   2025
  Planarity :  0.003   0.035   2240
  Dihedral  :  3.281  12.964   1710
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.37 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.22), residues: 1580
  helix:  2.54 (0.15), residues: 1030
  sheet:  1.27 (0.45), residues: 135
  loop :  0.11 (0.37), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 196 
 HIS   0.003   0.001   HIS C 331 
 PHE   0.012   0.001   PHE C 352 
 TYR   0.010   0.001   TYR C 299 
 ARG   0.003   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 1.477 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8618 (tpt) cc_final: 0.8120 (tpt)
REVERT: B  292 MET cc_start: 0.7107 (mtt) cc_final: 0.6808 (mtt)
REVERT: B  336 MET cc_start: 0.8098 (mmt) cc_final: 0.7447 (mmt)
REVERT: C  124 MET cc_start: 0.8697 (tpt) cc_final: 0.8427 (tpt)
  outliers start: 32
  outliers final: 29
  residues processed: 105
  average time/residue: 0.2221
  time to fit residues: 37.3602
Evaluate side-chains
  108 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  232 HIS
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  265 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 94 optimal weight:    8.9990
   chunk 101 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
B 122 HIS
C 122 HIS
D 122 HIS
E 122 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13025  Z= 0.317
  Angle     :  0.533   6.597  17595  Z= 0.274
  Chirality :  0.041   0.146   2025
  Planarity :  0.003   0.037   2240
  Dihedral  :  3.549  13.101   1710
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.66 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.22), residues: 1580
  helix:  2.15 (0.15), residues: 1030
  sheet:  1.36 (0.47), residues: 135
  loop :  0.22 (0.37), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.015   0.002   PHE A 352 
 TYR   0.020   0.002   TYR B 299 
 ARG   0.003   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 1.505 
Fit side-chains
REVERT: B  292 MET cc_start: 0.7260 (mtt) cc_final: 0.6922 (mtt)
REVERT: C  124 MET cc_start: 0.8728 (tpt) cc_final: 0.8291 (tpt)
REVERT: E  228 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7535 (mtm180)
  outliers start: 43
  outliers final: 39
  residues processed: 113
  average time/residue: 0.2048
  time to fit residues: 37.0254
Evaluate side-chains
  116 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 77
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  232 HIS
Chi-restraints excluded: chain D residue  274 SER
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue   99 SER
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  342 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 143 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9980
   chunk 139 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   chunk 109 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9980
   chunk 138 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13025  Z= 0.203
  Angle     :  0.474   6.683  17595  Z= 0.245
  Chirality :  0.038   0.138   2025
  Planarity :  0.003   0.036   2240
  Dihedral  :  3.434  13.452   1710
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.30 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.22), residues: 1580
  helix:  2.31 (0.15), residues: 1030
  sheet:  1.69 (0.45), residues: 145
  loop :  0.15 (0.38), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.013   0.001   PHE A 352 
 TYR   0.015   0.001   TYR E 299 
 ARG   0.003   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 1.568 
Fit side-chains
REVERT: B  292 MET cc_start: 0.7187 (mtt) cc_final: 0.6855 (mtt)
REVERT: C  124 MET cc_start: 0.8719 (tpt) cc_final: 0.8443 (tpt)
  outliers start: 39
  outliers final: 39
  residues processed: 110
  average time/residue: 0.1981
  time to fit residues: 35.1744
Evaluate side-chains
  113 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 74
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  232 HIS
Chi-restraints excluded: chain D residue  274 SER
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  274 SER
Chi-restraints excluded: chain E residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 147 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0670
   chunk 154 optimal weight:    0.9980
   chunk 142 optimal weight:    0.9990
   chunk 122 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.7320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13025  Z= 0.179
  Angle     :  0.457   6.798  17595  Z= 0.237
  Chirality :  0.038   0.139   2025
  Planarity :  0.003   0.035   2240
  Dihedral  :  3.365  13.473   1710
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.37 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.22), residues: 1580
  helix:  2.43 (0.15), residues: 1030
  sheet:  1.34 (0.47), residues: 135
  loop :  0.18 (0.37), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.013   0.001   PHE D 352 
 TYR   0.013   0.001   TYR E 299 
 ARG   0.003   0.000   ARG B 102 

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

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

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3160 Ramachandran restraints generated.
    1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 78
  time to evaluate  : 1.408 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8625 (tpt) cc_final: 0.8122 (tpt)
REVERT: B  292 MET cc_start: 0.7155 (mtt) cc_final: 0.6825 (mtt)
REVERT: C  124 MET cc_start: 0.8704 (tpt) cc_final: 0.8436 (tpt)
  outliers start: 39
  outliers final: 38
  residues processed: 111
  average time/residue: 0.1900
  time to fit residues: 33.9767
Evaluate side-chains
  115 residues out of total 1455 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 77
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  206 ILE
Chi-restraints excluded: chain D residue  232 HIS
Chi-restraints excluded: chain D residue  274 SER
Chi-restraints excluded: chain D residue  383 MET
Chi-restraints excluded: chain E residue   86 PHE
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  206 ILE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  274 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 113 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   chunk 123 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 126 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.196238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.136372 restraints weight = 12077.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.19
r_work: 0.3029 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13025  Z= 0.313
  Angle     :  0.541   6.728  17595  Z= 0.278
  Chirality :  0.041   0.147   2025
  Planarity :  0.003   0.037   2240
  Dihedral  :  3.615  13.547   1710
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.09 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.22), residues: 1580
  helix:  2.07 (0.15), residues: 1030
  sheet:  1.74 (0.45), residues: 145
  loop :  0.23 (0.38), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.015   0.002   PHE D 352 
 TYR   0.020   0.002   TYR B 299 
 ARG   0.003   0.000   ARG E 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2248.41 seconds
wall clock time: 41 minutes 44.86 seconds (2504.86 seconds total)