Starting phenix.real_space_refine
on Thu Feb  5 03:09:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/02_2026/8io0_35603.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.023
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       4      5.49       5
     S     104      5.16       5
     C    9630      2.51       5
     N    2503      2.21       5
     O    2487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14728
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3654
          Classifications: {'peptide': 473}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 18, 'TRANS': 454}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 285
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 163
    Chain: "B"
      Number of atoms: 3662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3662
          Classifications: {'peptide': 474}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 18, 'TRANS': 455}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 285
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 163
    Chain: "C"
      Number of atoms: 3662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3662
          Classifications: {'peptide': 474}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 18, 'TRANS': 455}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 285
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 163
    Chain: "D"
      Number of atoms: 3662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3662
          Classifications: {'peptide': 474}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 18, 'TRANS': 455}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 285
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 163
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "D"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 3.46, per 1000 atoms: 0.23
  Number of scatterers: 14728
  At special positions: 0
  Unit cell: (100.2, 100.2, 122.912, 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     104     16.00
     P       4     15.00
     O    2487      8.00
     N    2503      7.00
     C    9630      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  - 3.00
        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: 1.36
  Conformation dependent library (CDL) restraints added in 627.9 milliseconds
  

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3598

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 8 sheets defined
      73.7% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 54
      removed outlier: 4.263A  pdb=" N   LEU A  53 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 66
    Processing helix  chain 'A' and resid 67 through 79
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 3.511A  pdb=" N   PHE A  94 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE A  99 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      Proline residue:  A 112  - end of helix
    Processing helix  chain 'A' and resid 123 through 146
      removed outlier: 3.867A  pdb=" N   LEU A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 171
      removed outlier: 3.725A  pdb=" N   ILE A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG A 165 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 182 through 191
      removed outlier: 3.884A  pdb=" N   ILE A 186 " --> pdb=" O   PRO A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
    Processing helix  chain 'A' and resid 219 through 222
      removed outlier: 3.637A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 219 through 222'
    Processing helix  chain 'A' and resid 223 through 238
    Processing helix  chain 'A' and resid 245 through 276
      removed outlier: 3.644A  pdb=" N   VAL A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS A 267 " --> pdb=" O   HIS A 263 " (cutoff:3.500A)
      Proline residue:  A 273  - end of helix
      removed outlier: 3.608A  pdb=" N   GLN A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 293 through 310
    Processing helix  chain 'A' and resid 321 through 351
      removed outlier: 3.575A  pdb=" N   TRP A 326 " --> pdb=" O   MET A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 374
      removed outlier: 3.538A  pdb=" N   TYR A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS A 374 " --> pdb=" O   TYR A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 392
    Processing helix  chain 'A' and resid 398 through 406
      removed outlier: 3.522A  pdb=" N   LEU A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 426
      removed outlier: 5.990A  pdb=" N   GLY A 421 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 432
      removed outlier: 3.619A  pdb=" N   HIS A 431 " --> pdb=" O   PRO A 427 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
    Processing helix  chain 'A' and resid 493 through 499
      removed outlier: 3.884A  pdb=" N   LEU A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 529
    Processing helix  chain 'A' and resid 530 through 546
      removed outlier: 3.792A  pdb=" N   ARG A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
      removed outlier: 4.263A  pdb=" N   LEU B  53 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 66
    Processing helix  chain 'B' and resid 67 through 79
    Processing helix  chain 'B' and resid 90 through 117
      removed outlier: 3.511A  pdb=" N   PHE B  94 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE B  99 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 123 through 146
      removed outlier: 3.867A  pdb=" N   LEU B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 171
      removed outlier: 3.725A  pdb=" N   ILE B 164 " --> pdb=" O   ALA B 160 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 181
    Processing helix  chain 'B' and resid 182 through 191
      removed outlier: 3.884A  pdb=" N   ILE B 186 " --> pdb=" O   PRO B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 218
    Processing helix  chain 'B' and resid 219 through 222
      removed outlier: 3.637A  pdb=" N   LEU B 222 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 219 through 222'
    Processing helix  chain 'B' and resid 223 through 238
    Processing helix  chain 'B' and resid 245 through 276
      removed outlier: 3.644A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS B 267 " --> pdb=" O   HIS B 263 " (cutoff:3.500A)
      Proline residue:  B 273  - end of helix
      removed outlier: 3.608A  pdb=" N   GLN B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 293 through 310
    Processing helix  chain 'B' and resid 321 through 351
      removed outlier: 3.575A  pdb=" N   TRP B 326 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 374
      removed outlier: 3.538A  pdb=" N   TYR B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS B 374 " --> pdb=" O   TYR B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 392
    Processing helix  chain 'B' and resid 398 through 406
      removed outlier: 3.522A  pdb=" N   LEU B 406 " --> pdb=" O   ILE B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 426
      removed outlier: 5.990A  pdb=" N   GLY B 421 " --> pdb=" O   PHE B 417 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 432
      removed outlier: 3.619A  pdb=" N   HIS B 431 " --> pdb=" O   PRO B 427 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA B 432 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 442
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.884A  pdb=" N   LEU B 497 " --> pdb=" O   GLU B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 529
    Processing helix  chain 'B' and resid 530 through 546
      removed outlier: 3.791A  pdb=" N   ARG B 534 " --> pdb=" O   PRO B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 54
      removed outlier: 4.263A  pdb=" N   LEU C  53 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 66
    Processing helix  chain 'C' and resid 67 through 79
    Processing helix  chain 'C' and resid 90 through 117
      removed outlier: 3.511A  pdb=" N   PHE C  94 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE C  99 " --> pdb=" O   TYR C  95 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU C 102 " --> pdb=" O   LEU C  98 " (cutoff:3.500A)
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 123 through 146
      removed outlier: 3.867A  pdb=" N   LEU C 141 " --> pdb=" O   PHE C 137 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 171
      removed outlier: 3.725A  pdb=" N   ILE C 164 " --> pdb=" O   ALA C 160 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG C 165 " --> pdb=" O   PRO C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 181
    Processing helix  chain 'C' and resid 182 through 191
      removed outlier: 3.884A  pdb=" N   ILE C 186 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 218
    Processing helix  chain 'C' and resid 219 through 222
      removed outlier: 3.637A  pdb=" N   LEU C 222 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 219 through 222'
    Processing helix  chain 'C' and resid 223 through 238
    Processing helix  chain 'C' and resid 245 through 276
      removed outlier: 3.644A  pdb=" N   VAL C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS C 267 " --> pdb=" O   HIS C 263 " (cutoff:3.500A)
      Proline residue:  C 273  - end of helix
      removed outlier: 3.608A  pdb=" N   GLN C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 293 through 310
    Processing helix  chain 'C' and resid 321 through 351
      removed outlier: 3.575A  pdb=" N   TRP C 326 " --> pdb=" O   MET C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 374
      removed outlier: 3.538A  pdb=" N   TYR C 360 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS C 374 " --> pdb=" O   TYR C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 377 through 392
    Processing helix  chain 'C' and resid 398 through 406
      removed outlier: 3.522A  pdb=" N   LEU C 406 " --> pdb=" O   ILE C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 426
      removed outlier: 5.990A  pdb=" N   GLY C 421 " --> pdb=" O   PHE C 417 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU C 422 " --> pdb=" O   THR C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 426 through 432
      removed outlier: 3.619A  pdb=" N   HIS C 431 " --> pdb=" O   PRO C 427 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA C 432 " --> pdb=" O   LEU C 428 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 442
    Processing helix  chain 'C' and resid 493 through 499
      removed outlier: 3.884A  pdb=" N   LEU C 497 " --> pdb=" O   GLU C 493 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 519 through 529
    Processing helix  chain 'C' and resid 530 through 546
      removed outlier: 3.792A  pdb=" N   ARG C 534 " --> pdb=" O   PRO C 530 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 54
      removed outlier: 4.263A  pdb=" N   LEU D  53 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 66
    Processing helix  chain 'D' and resid 67 through 79
    Processing helix  chain 'D' and resid 90 through 117
      removed outlier: 3.511A  pdb=" N   PHE D  94 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE D  99 " --> pdb=" O   TYR D  95 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU D 102 " --> pdb=" O   LEU D  98 " (cutoff:3.500A)
      Proline residue:  D 112  - end of helix
    Processing helix  chain 'D' and resid 123 through 146
      removed outlier: 3.867A  pdb=" N   LEU D 141 " --> pdb=" O   PHE D 137 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG D 146 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 171
      removed outlier: 3.725A  pdb=" N   ILE D 164 " --> pdb=" O   ALA D 160 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG D 165 " --> pdb=" O   PRO D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 181
    Processing helix  chain 'D' and resid 182 through 191
      removed outlier: 3.884A  pdb=" N   ILE D 186 " --> pdb=" O   PRO D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 218
    Processing helix  chain 'D' and resid 219 through 222
      removed outlier: 3.637A  pdb=" N   LEU D 222 " --> pdb=" O   LEU D 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 219 through 222'
    Processing helix  chain 'D' and resid 223 through 238
    Processing helix  chain 'D' and resid 245 through 276
      removed outlier: 3.644A  pdb=" N   VAL D 249 " --> pdb=" O   ALA D 245 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS D 267 " --> pdb=" O   HIS D 263 " (cutoff:3.500A)
      Proline residue:  D 273  - end of helix
      removed outlier: 3.608A  pdb=" N   GLN D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 287
    Processing helix  chain 'D' and resid 293 through 310
    Processing helix  chain 'D' and resid 321 through 351
      removed outlier: 3.575A  pdb=" N   TRP D 326 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 354 through 374
      removed outlier: 3.538A  pdb=" N   TYR D 360 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS D 374 " --> pdb=" O   TYR D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 377 through 392
    Processing helix  chain 'D' and resid 398 through 406
      removed outlier: 3.522A  pdb=" N   LEU D 406 " --> pdb=" O   ILE D 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 407 through 426
      removed outlier: 5.990A  pdb=" N   GLY D 421 " --> pdb=" O   PHE D 417 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU D 422 " --> pdb=" O   THR D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 432
      removed outlier: 3.619A  pdb=" N   HIS D 431 " --> pdb=" O   PRO D 427 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA D 432 " --> pdb=" O   LEU D 428 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 442
    Processing helix  chain 'D' and resid 493 through 499
      removed outlier: 3.884A  pdb=" N   LEU D 497 " --> pdb=" O   GLU D 493 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 519 through 529
    Processing helix  chain 'D' and resid 530 through 546
      removed outlier: 3.791A  pdb=" N   ARG D 534 " --> pdb=" O   PRO D 530 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 449
    Processing sheet with id=AA2, first strand: chain 'A' and resid 454 through 456
      removed outlier: 6.699A  pdb=" N   LEU A 454 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ALA A 508 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL A 456 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 449
    Processing sheet with id=AA4, first strand: chain 'B' and resid 454 through 456
      removed outlier: 6.699A  pdb=" N   LEU B 454 " --> pdb=" O   ALA B 508 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ALA B 508 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL B 456 " --> pdb=" O   VAL B 506 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 445 through 449
    Processing sheet with id=AA6, first strand: chain 'C' and resid 454 through 456
      removed outlier: 6.699A  pdb=" N   LEU C 454 " --> pdb=" O   ALA C 508 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ALA C 508 " --> pdb=" O   LEU C 454 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL C 456 " --> pdb=" O   VAL C 506 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 449
    Processing sheet with id=AA8, first strand: chain 'D' and resid 454 through 456
      removed outlier: 6.699A  pdb=" N   LEU D 454 " --> pdb=" O   ALA D 508 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ALA D 508 " --> pdb=" O   LEU D 454 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL D 456 " --> pdb=" O   VAL D 506 " (cutoff:3.500A)

    970 hydrogen bonds defined for protein.
    2853 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: 2.79

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4574
        1.34 -     1.46: 3876
        1.46 -     1.58: 6490
        1.58 -     1.70: 8
        1.70 -     1.82: 176
  Bond restraints: 15124
  Sorted by residual:
  bond pdb=" C   PRO A 124 "
       pdb=" N   PRO A 125 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.32e+00
  bond pdb=" C   PRO C 124 "
       pdb=" N   PRO C 125 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.32e+00
  bond pdb=" C   PRO D 124 "
       pdb=" N   PRO D 125 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.32e+00
  bond pdb=" C   PRO B 124 "
       pdb=" N   PRO B 125 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.32e+00
  bond pdb=" C4' CMP B 801 "
       pdb=" O4' CMP B 801 "
    ideal  model  delta    sigma   weight residual
    1.454  1.423  0.031 1.50e-02 4.44e+03 4.18e+00
  ... (remaining 15119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 19586
        1.93 -     3.85: 835
        3.85 -     5.78: 136
        5.78 -     7.70: 48
        7.70 -     9.63: 8
  Bond angle restraints: 20613
  Sorted by residual:
  angle pdb=" C5' CMP B 801 "
        pdb=" C4' CMP B 801 "
        pdb=" O4' CMP B 801 "
      ideal   model   delta    sigma   weight residual
     109.10  115.71   -6.61 1.50e+00 4.44e-01 1.94e+01
  angle pdb=" C5' CMP A 801 "
        pdb=" C4' CMP A 801 "
        pdb=" O4' CMP A 801 "
      ideal   model   delta    sigma   weight residual
     109.10  115.71   -6.61 1.50e+00 4.44e-01 1.94e+01
  angle pdb=" C5' CMP D 801 "
        pdb=" C4' CMP D 801 "
        pdb=" O4' CMP D 801 "
      ideal   model   delta    sigma   weight residual
     109.10  115.71   -6.61 1.50e+00 4.44e-01 1.94e+01
  angle pdb=" C5' CMP C 801 "
        pdb=" C4' CMP C 801 "
        pdb=" O4' CMP C 801 "
      ideal   model   delta    sigma   weight residual
     109.10  115.71   -6.61 1.50e+00 4.44e-01 1.94e+01
  angle pdb=" C1' CMP D 801 "
        pdb=" O4' CMP D 801 "
        pdb=" C4' CMP D 801 "
      ideal   model   delta    sigma   weight residual
     109.70  105.43    4.27 1.00e+00 1.00e+00 1.83e+01
  ... (remaining 20608 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.79: 8739
       34.79 -    69.58: 16
       69.58 -   104.36: 16
      104.36 -   139.15: 0
      139.15 -   173.94: 12
  Dihedral angle restraints: 8783
    sinusoidal: 3230
      harmonic: 5553
  Sorted by residual:
  dihedral pdb=" C3' CMP D 801 "
           pdb=" O3' CMP D 801 "
           pdb=" P   CMP D 801 "
           pdb=" O1P CMP D 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.94 -173.94     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C3' CMP C 801 "
           pdb=" O3' CMP C 801 "
           pdb=" P   CMP C 801 "
           pdb=" O1P CMP C 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.94 -173.94     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C3' CMP B 801 "
           pdb=" O3' CMP B 801 "
           pdb=" P   CMP B 801 "
           pdb=" O1P CMP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  113.94 -173.94     1      2.00e+01 2.50e-03 4.79e+01
  ... (remaining 8780 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1722
       0.054 -    0.108: 528
       0.108 -    0.162: 112
       0.162 -    0.215: 12
       0.215 -    0.269: 4
  Chirality restraints: 2378
  Sorted by residual:
  chirality pdb=" C1' CMP A 801 "
            pdb=" C2' CMP A 801 "
            pdb=" N9  CMP A 801 "
            pdb=" O4' CMP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.17    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C1' CMP B 801 "
            pdb=" C2' CMP B 801 "
            pdb=" N9  CMP B 801 "
            pdb=" O4' CMP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.17    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C1' CMP C 801 "
            pdb=" C2' CMP C 801 "
            pdb=" N9  CMP C 801 "
            pdb=" O4' CMP C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.17    0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 2375 not shown)

  Planarity restraints: 2543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 234 "   -0.034 2.00e-02 2.50e+03   2.05e-02 1.05e+01
        pdb=" CG  TRP B 234 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 234 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 234 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 234 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 234 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 234 "   -0.034 2.00e-02 2.50e+03   2.05e-02 1.05e+01
        pdb=" CG  TRP D 234 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 234 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 234 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 234 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 234 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 234 "   -0.034 2.00e-02 2.50e+03   2.05e-02 1.05e+01
        pdb=" CG  TRP A 234 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 234 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 234 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 234 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 234 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2540 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 4024
        2.80 -     3.32: 13646
        3.32 -     3.85: 23970
        3.85 -     4.37: 25612
        4.37 -     4.90: 45142
  Nonbonded interactions: 112394
  Sorted by model distance:
  nonbonded pdb=" O   VAL C 475 "
            pdb=" OG1 THR C 483 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL D 475 "
            pdb=" OG1 THR D 483 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL B 475 "
            pdb=" OG1 THR B 483 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL A 475 "
            pdb=" OG1 THR A 483 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ARG B 167 "
            pdb=" OG1 THR B 171 "
     model   vdw
     2.329 3.040
  ... (remaining 112389 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'
  selection = (chain 'B' and (resid 50 through 475 or resid 483 through 801))
  selection = (chain 'C' and (resid 50 through 475 or resid 483 through 801))
  selection = (chain 'D' and (resid 50 through 475 or resid 483 through 801))
}

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:             0.540
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.110
  Find NCS groups from input model:        0.290
  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:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
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      :  0.008   0.096  15124  Z= 0.372
  Angle     :  0.965   9.629  20613  Z= 0.547
  Chirality :  0.053   0.269   2378
  Planarity :  0.007   0.062   2543
  Dihedral  : 12.292 173.940   5185
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.08 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.16), residues: 1863
  helix: -1.00 (0.12), residues: 1244
  sheet:  0.41 (0.64), residues: 48
  loop : -2.01 (0.23), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 420 
 TYR   0.024   0.003   TYR D 511 
 PHE   0.048   0.003   PHE D 238 
 TRP   0.053   0.003   TRP B 234 
 HIS   0.016   0.003   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00845 (15124)
  covalent geometry    : angle       0.96509 (20613)
  hydrogen bonds       : bond        0.15747 (  970)
  hydrogen bonds       : angle       5.81752 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 184
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  100 MET cc_start: 0.8915 (mmm) cc_final: 0.8283 (tpp)
REVERT: A  257 MET cc_start: 0.9138 (tpp) cc_final: 0.8837 (tpp)
REVERT: A  365 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9090 (tttt)
REVERT: A  386 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9087 (mt-10)
REVERT: A  389 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: A  395 LYS cc_start: 0.8503 (mttt) cc_final: 0.7895 (mtpt)
REVERT: A  443 LYS cc_start: 0.9623 (mttt) cc_final: 0.9309 (mtmt)
REVERT: A  465 MET cc_start: 0.9347 (ttm) cc_final: 0.9077 (ttt)
REVERT: A  485 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (pt)
REVERT: A  537 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9267 (mp0)
REVERT: A  541 MET cc_start: 0.9709 (mmm) cc_final: 0.9432 (mmm)
REVERT: B  100 MET cc_start: 0.8910 (mmm) cc_final: 0.8283 (tpp)
REVERT: B  257 MET cc_start: 0.9138 (tpp) cc_final: 0.8838 (tpp)
REVERT: B  365 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9091 (tttt)
REVERT: B  386 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9086 (mt-10)
REVERT: B  389 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8167 (mt-10)
REVERT: B  395 LYS cc_start: 0.8498 (mttt) cc_final: 0.7891 (mtpt)
REVERT: B  443 LYS cc_start: 0.9625 (mttt) cc_final: 0.9315 (mtmt)
REVERT: B  465 MET cc_start: 0.9349 (ttm) cc_final: 0.9078 (ttt)
REVERT: B  485 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8408 (pt)
REVERT: B  537 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9265 (mp0)
REVERT: B  541 MET cc_start: 0.9708 (mmm) cc_final: 0.9430 (mmm)
REVERT: C  100 MET cc_start: 0.8909 (mmm) cc_final: 0.8277 (tpp)
REVERT: C  257 MET cc_start: 0.9141 (tpp) cc_final: 0.8839 (tpp)
REVERT: C  365 LYS cc_start: 0.9297 (mmtt) cc_final: 0.9091 (tttt)
REVERT: C  386 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9091 (mt-10)
REVERT: C  389 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8166 (mt-10)
REVERT: C  395 LYS cc_start: 0.8500 (mttt) cc_final: 0.7895 (mtpt)
REVERT: C  443 LYS cc_start: 0.9622 (mttt) cc_final: 0.9308 (mtmt)
REVERT: C  465 MET cc_start: 0.9345 (ttm) cc_final: 0.9075 (ttt)
REVERT: C  485 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (pt)
REVERT: C  537 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9265 (mp0)
REVERT: C  541 MET cc_start: 0.9711 (mmm) cc_final: 0.9434 (mmm)
REVERT: D  100 MET cc_start: 0.8906 (mmm) cc_final: 0.8274 (tpp)
REVERT: D  257 MET cc_start: 0.9139 (tpp) cc_final: 0.8839 (tpp)
REVERT: D  365 LYS cc_start: 0.9294 (mmtt) cc_final: 0.9089 (tttt)
REVERT: D  386 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9089 (mt-10)
REVERT: D  389 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8164 (mt-10)
REVERT: D  395 LYS cc_start: 0.8493 (mttt) cc_final: 0.7886 (mtpt)
REVERT: D  443 LYS cc_start: 0.9623 (mttt) cc_final: 0.9313 (mtmt)
REVERT: D  465 MET cc_start: 0.9349 (ttm) cc_final: 0.9078 (ttt)
REVERT: D  485 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8408 (pt)
REVERT: D  537 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9264 (mp0)
REVERT: D  541 MET cc_start: 0.9708 (mmm) cc_final: 0.9432 (mmm)
  outliers start: 4
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1805
  time to fit residues: 45.4141
Evaluate side-chains
  109 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   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 107 ASN
A 130 ASN
A 292 HIS
A 308 HIS
A 470 HIS
A 521 HIS
B 107 ASN
B 130 ASN
B 292 HIS
B 308 HIS
B 470 HIS
B 521 HIS
C 107 ASN
C 130 ASN
C 292 HIS
C 308 HIS
C 470 HIS
C 521 HIS
D 107 ASN
D 130 ASN
D 292 HIS
D 308 HIS
D 470 HIS
D 521 HIS

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.063892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.046214 restraints weight = 64413.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.91
r_work: 0.2737 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15124  Z= 0.146
  Angle     :  0.584   7.369  20613  Z= 0.309
  Chirality :  0.039   0.135   2378
  Planarity :  0.004   0.047   2543
  Dihedral  : 13.211 174.288   2103
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.90 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.19), residues: 1863
  helix:  1.20 (0.14), residues: 1292
  sheet:  1.16 (0.59), residues: 48
  loop : -1.56 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 463 
 TYR   0.011   0.001   TYR A  95 
 PHE   0.011   0.001   PHE B 270 
 TRP   0.016   0.001   TRP A 264 
 HIS   0.005   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15124)
  covalent geometry    : angle       0.58414 (20613)
  hydrogen bonds       : bond        0.04257 (  970)
  hydrogen bonds       : angle       3.82724 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9161 (mmm) cc_final: 0.8659 (tpp)
REVERT: A  257 MET cc_start: 0.9427 (tpp) cc_final: 0.9222 (tpp)
REVERT: A  395 LYS cc_start: 0.8213 (mttt) cc_final: 0.7632 (mtpt)
REVERT: A  426 MET cc_start: 0.8309 (mmm) cc_final: 0.8045 (tpp)
REVERT: A  465 MET cc_start: 0.9443 (ttm) cc_final: 0.9134 (ttt)
REVERT: A  485 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8139 (pt)
REVERT: A  541 MET cc_start: 0.9780 (mmm) cc_final: 0.9504 (mmm)
REVERT: B  100 MET cc_start: 0.9170 (mmm) cc_final: 0.8676 (tpp)
REVERT: B  257 MET cc_start: 0.9417 (tpp) cc_final: 0.9209 (tpp)
REVERT: B  395 LYS cc_start: 0.8200 (mttt) cc_final: 0.7627 (mtpt)
REVERT: B  426 MET cc_start: 0.8311 (mmm) cc_final: 0.8051 (tpp)
REVERT: B  465 MET cc_start: 0.9434 (ttm) cc_final: 0.9116 (ttt)
REVERT: B  485 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8243 (pt)
REVERT: B  541 MET cc_start: 0.9774 (mmm) cc_final: 0.9493 (mmm)
REVERT: C  100 MET cc_start: 0.9153 (mmm) cc_final: 0.8654 (tpp)
REVERT: C  257 MET cc_start: 0.9426 (tpp) cc_final: 0.9220 (tpp)
REVERT: C  395 LYS cc_start: 0.8213 (mttt) cc_final: 0.7636 (mtpt)
REVERT: C  426 MET cc_start: 0.8307 (mmm) cc_final: 0.8047 (tpp)
REVERT: C  465 MET cc_start: 0.9439 (ttm) cc_final: 0.9126 (ttt)
REVERT: C  485 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8242 (pt)
REVERT: C  541 MET cc_start: 0.9772 (mmm) cc_final: 0.9491 (mmm)
REVERT: D  100 MET cc_start: 0.9155 (mmm) cc_final: 0.8663 (tpp)
REVERT: D  257 MET cc_start: 0.9424 (tpp) cc_final: 0.9217 (tpp)
REVERT: D  395 LYS cc_start: 0.8210 (mttt) cc_final: 0.7636 (mtpt)
REVERT: D  426 MET cc_start: 0.8308 (mmm) cc_final: 0.8046 (tpp)
REVERT: D  465 MET cc_start: 0.9440 (ttm) cc_final: 0.9125 (ttt)
REVERT: D  485 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8244 (pt)
REVERT: D  541 MET cc_start: 0.9766 (mmm) cc_final: 0.9481 (mmm)
  outliers start: 4
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1417
  time to fit residues: 25.5800
Evaluate side-chains
  116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0980
   chunk 121 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 172 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 82 optimal weight:    3.9990
   chunk 155 optimal weight:    9.9990
   chunk 175 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    2.6188

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.063897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.046386 restraints weight = 65334.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.01
r_work: 0.2735 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15124  Z= 0.147
  Angle     :  0.550   7.463  20613  Z= 0.287
  Chirality :  0.038   0.115   2378
  Planarity :  0.004   0.047   2543
  Dihedral  : 12.815 170.596   2103
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  5.69 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.19), residues: 1863
  helix:  2.11 (0.14), residues: 1296
  sheet:  1.79 (0.60), residues: 48
  loop : -1.10 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 507 
 TYR   0.011   0.001   TYR B 511 
 PHE   0.011   0.001   PHE A 270 
 TRP   0.014   0.001   TRP D 264 
 HIS   0.004   0.001   HIS D 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (15124)
  covalent geometry    : angle       0.54981 (20613)
  hydrogen bonds       : bond        0.03689 (  970)
  hydrogen bonds       : angle       3.44717 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.9407 (tpp) cc_final: 0.9199 (tpp)
REVERT: A  365 LYS cc_start: 0.9407 (tttt) cc_final: 0.9161 (tttt)
REVERT: A  426 MET cc_start: 0.8450 (mmm) cc_final: 0.8156 (tpp)
REVERT: A  485 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (pp)
REVERT: A  531 MET cc_start: 0.9052 (pmm) cc_final: 0.8541 (pmm)
REVERT: A  541 MET cc_start: 0.9786 (mmm) cc_final: 0.9521 (mmm)
REVERT: B  257 MET cc_start: 0.9394 (tpp) cc_final: 0.9184 (tpp)
REVERT: B  365 LYS cc_start: 0.9408 (tttt) cc_final: 0.9163 (tttt)
REVERT: B  426 MET cc_start: 0.8450 (mmm) cc_final: 0.8155 (tpp)
REVERT: B  485 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8416 (pp)
REVERT: B  531 MET cc_start: 0.9051 (pmm) cc_final: 0.8539 (pmm)
REVERT: B  541 MET cc_start: 0.9782 (mmm) cc_final: 0.9513 (mmm)
REVERT: C  100 MET cc_start: 0.9167 (mmm) cc_final: 0.8967 (mmm)
REVERT: C  257 MET cc_start: 0.9392 (tpp) cc_final: 0.9179 (tpp)
REVERT: C  365 LYS cc_start: 0.9410 (tttt) cc_final: 0.9164 (tttt)
REVERT: C  426 MET cc_start: 0.8452 (mmm) cc_final: 0.8165 (tpp)
REVERT: C  485 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8416 (pp)
REVERT: C  531 MET cc_start: 0.9067 (pmm) cc_final: 0.8560 (pmm)
REVERT: C  541 MET cc_start: 0.9784 (mmm) cc_final: 0.9516 (mmm)
REVERT: D  257 MET cc_start: 0.9401 (tpp) cc_final: 0.9194 (tpp)
REVERT: D  365 LYS cc_start: 0.9409 (tttt) cc_final: 0.9162 (tttt)
REVERT: D  426 MET cc_start: 0.8452 (mmm) cc_final: 0.8162 (tpp)
REVERT: D  485 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8415 (pp)
REVERT: D  531 MET cc_start: 0.9069 (pmm) cc_final: 0.8562 (pmm)
REVERT: D  541 MET cc_start: 0.9783 (mmm) cc_final: 0.9515 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 120
  average time/residue: 0.1486
  time to fit residues: 25.8662
Evaluate side-chains
  112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 150 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.063891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.046400 restraints weight = 65180.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 3.96
r_work: 0.2735 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15124  Z= 0.142
  Angle     :  0.534   7.532  20613  Z= 0.278
  Chirality :  0.038   0.117   2378
  Planarity :  0.003   0.041   2543
  Dihedral  : 12.635 168.759   2103
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  5.15 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.20), residues: 1863
  helix:  2.50 (0.14), residues: 1296
  sheet:  1.99 (0.61), residues: 48
  loop : -0.88 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 463 
 TYR   0.011   0.001   TYR D 511 
 PHE   0.010   0.001   PHE D 270 
 TRP   0.011   0.001   TRP A 264 
 HIS   0.003   0.001   HIS C 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15124)
  covalent geometry    : angle       0.53410 (20613)
  hydrogen bonds       : bond        0.03470 (  970)
  hydrogen bonds       : angle       3.33541 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9067 (mmm) cc_final: 0.8725 (tpp)
REVERT: A  240 MET cc_start: 0.8181 (tpp) cc_final: 0.7685 (tpp)
REVERT: A  257 MET cc_start: 0.9367 (tpp) cc_final: 0.9145 (tpp)
REVERT: A  365 LYS cc_start: 0.9402 (tttt) cc_final: 0.9172 (tttt)
REVERT: A  395 LYS cc_start: 0.8330 (mttt) cc_final: 0.7912 (mtmm)
REVERT: A  485 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8164 (pp)
REVERT: A  531 MET cc_start: 0.9008 (pmm) cc_final: 0.8636 (pmm)
REVERT: A  532 MET cc_start: 0.9414 (mmm) cc_final: 0.9150 (mmp)
REVERT: A  541 MET cc_start: 0.9779 (mmm) cc_final: 0.9507 (mmm)
REVERT: B  100 MET cc_start: 0.9074 (mmm) cc_final: 0.8736 (tpp)
REVERT: B  240 MET cc_start: 0.8178 (tpp) cc_final: 0.7680 (tpp)
REVERT: B  257 MET cc_start: 0.9358 (tpp) cc_final: 0.9133 (tpp)
REVERT: B  365 LYS cc_start: 0.9402 (tttt) cc_final: 0.9172 (tttt)
REVERT: B  395 LYS cc_start: 0.8336 (mttt) cc_final: 0.7921 (mtmm)
REVERT: B  485 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8449 (pp)
REVERT: B  531 MET cc_start: 0.9012 (pmm) cc_final: 0.8616 (pmm)
REVERT: B  532 MET cc_start: 0.9412 (mmm) cc_final: 0.9137 (mmp)
REVERT: B  541 MET cc_start: 0.9776 (mmm) cc_final: 0.9502 (mmm)
REVERT: C  100 MET cc_start: 0.9180 (mmm) cc_final: 0.8921 (mmm)
REVERT: C  240 MET cc_start: 0.8164 (tpp) cc_final: 0.7667 (tpp)
REVERT: C  257 MET cc_start: 0.9360 (tpp) cc_final: 0.9134 (tpp)
REVERT: C  365 LYS cc_start: 0.9404 (tttt) cc_final: 0.9173 (tttt)
REVERT: C  395 LYS cc_start: 0.8330 (mttt) cc_final: 0.7917 (mtmm)
REVERT: C  485 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8448 (pp)
REVERT: C  531 MET cc_start: 0.9023 (pmm) cc_final: 0.8629 (pmm)
REVERT: C  532 MET cc_start: 0.9417 (mmm) cc_final: 0.9139 (mmp)
REVERT: C  541 MET cc_start: 0.9776 (mmm) cc_final: 0.9501 (mmm)
REVERT: D  100 MET cc_start: 0.9064 (mmm) cc_final: 0.8727 (tpp)
REVERT: D  240 MET cc_start: 0.8164 (tpp) cc_final: 0.7665 (tpp)
REVERT: D  257 MET cc_start: 0.9368 (tpp) cc_final: 0.9144 (tpp)
REVERT: D  365 LYS cc_start: 0.9404 (tttt) cc_final: 0.9175 (tttt)
REVERT: D  395 LYS cc_start: 0.8340 (mttt) cc_final: 0.7932 (mtmm)
REVERT: D  485 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8446 (pp)
REVERT: D  531 MET cc_start: 0.9023 (pmm) cc_final: 0.8629 (pmm)
REVERT: D  532 MET cc_start: 0.9414 (mmm) cc_final: 0.9135 (mmp)
REVERT: D  541 MET cc_start: 0.9777 (mmm) cc_final: 0.9504 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1459
  time to fit residues: 24.9267
Evaluate side-chains
  109 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 22 optimal weight:    0.1980
   chunk 25 optimal weight:    7.9990
   chunk 115 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 152 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 155 optimal weight:    0.9980
   overall best weight:    2.8386

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.063364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046043 restraints weight = 64470.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 3.90
r_work: 0.2724 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15124  Z= 0.148
  Angle     :  0.543   7.565  20613  Z= 0.280
  Chirality :  0.038   0.117   2378
  Planarity :  0.003   0.041   2543
  Dihedral  : 12.549 168.350   2103
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.81 %
    Favored  : 94.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.20), residues: 1863
  helix:  2.68 (0.15), residues: 1296
  sheet:  2.23 (0.65), residues: 48
  loop : -0.68 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 420 
 TYR   0.010   0.001   TYR A 511 
 PHE   0.010   0.001   PHE A 270 
 TRP   0.011   0.001   TRP C 264 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (15124)
  covalent geometry    : angle       0.54287 (20613)
  hydrogen bonds       : bond        0.03525 (  970)
  hydrogen bonds       : angle       3.31177 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9059 (mmm) cc_final: 0.8660 (tpp)
REVERT: A  257 MET cc_start: 0.9394 (tpp) cc_final: 0.9182 (tpp)
REVERT: A  365 LYS cc_start: 0.9429 (tttt) cc_final: 0.9199 (tttt)
REVERT: A  395 LYS cc_start: 0.8373 (mttt) cc_final: 0.7967 (mtmm)
REVERT: A  485 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8178 (pp)
REVERT: A  494 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8951 (pt)
REVERT: A  531 MET cc_start: 0.9072 (pmm) cc_final: 0.8761 (pmm)
REVERT: A  532 MET cc_start: 0.9417 (mmm) cc_final: 0.9118 (mmp)
REVERT: A  541 MET cc_start: 0.9776 (mmm) cc_final: 0.9499 (mmm)
REVERT: B  100 MET cc_start: 0.9069 (mmm) cc_final: 0.8674 (tpp)
REVERT: B  257 MET cc_start: 0.9391 (tpp) cc_final: 0.9178 (tpp)
REVERT: B  365 LYS cc_start: 0.9427 (tttt) cc_final: 0.9196 (tttt)
REVERT: B  395 LYS cc_start: 0.8373 (mttt) cc_final: 0.7968 (mtmm)
REVERT: B  485 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8488 (pp)
REVERT: B  494 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8946 (pt)
REVERT: B  531 MET cc_start: 0.9080 (pmm) cc_final: 0.8766 (pmm)
REVERT: B  532 MET cc_start: 0.9416 (mmm) cc_final: 0.9118 (mmp)
REVERT: B  541 MET cc_start: 0.9774 (mmm) cc_final: 0.9496 (mmm)
REVERT: C  100 MET cc_start: 0.9191 (mmm) cc_final: 0.8891 (mmm)
REVERT: C  257 MET cc_start: 0.9395 (tpp) cc_final: 0.9179 (tpp)
REVERT: C  365 LYS cc_start: 0.9429 (tttt) cc_final: 0.9197 (tttt)
REVERT: C  395 LYS cc_start: 0.8367 (mttt) cc_final: 0.7966 (mtmm)
REVERT: C  485 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8490 (pp)
REVERT: C  494 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8950 (pt)
REVERT: C  531 MET cc_start: 0.9086 (pmm) cc_final: 0.8776 (pmm)
REVERT: C  532 MET cc_start: 0.9416 (mmm) cc_final: 0.9113 (mmp)
REVERT: C  541 MET cc_start: 0.9775 (mmm) cc_final: 0.9496 (mmm)
REVERT: D  100 MET cc_start: 0.9063 (mmm) cc_final: 0.8672 (tpp)
REVERT: D  257 MET cc_start: 0.9402 (tpp) cc_final: 0.9188 (tpp)
REVERT: D  365 LYS cc_start: 0.9430 (tttt) cc_final: 0.9200 (tttt)
REVERT: D  395 LYS cc_start: 0.8374 (mttt) cc_final: 0.7975 (mtmm)
REVERT: D  485 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8489 (pp)
REVERT: D  494 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8950 (pt)
REVERT: D  531 MET cc_start: 0.9083 (pmm) cc_final: 0.8771 (pmm)
REVERT: D  532 MET cc_start: 0.9410 (mmm) cc_final: 0.9111 (mmp)
REVERT: D  541 MET cc_start: 0.9776 (mmm) cc_final: 0.9498 (mmm)
  outliers start: 16
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1337
  time to fit residues: 23.0361
Evaluate side-chains
  116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  494 ILE
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  494 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 133 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 151 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 164 optimal weight:    0.9990
   chunk 156 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.063459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.046001 restraints weight = 65302.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.93
r_work: 0.2719 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15124  Z= 0.146
  Angle     :  0.534   7.579  20613  Z= 0.276
  Chirality :  0.038   0.117   2378
  Planarity :  0.003   0.042   2543
  Dihedral  : 12.524 168.505   2103
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.08 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.20), residues: 1863
  helix:  2.75 (0.14), residues: 1296
  sheet:  2.53 (0.70), residues: 48
  loop : -0.58 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 420 
 TYR   0.009   0.001   TYR A 511 
 PHE   0.010   0.001   PHE A 270 
 TRP   0.013   0.001   TRP C 264 
 HIS   0.003   0.001   HIS C 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (15124)
  covalent geometry    : angle       0.53402 (20613)
  hydrogen bonds       : bond        0.03460 (  970)
  hydrogen bonds       : angle       3.27826 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9068 (mmm) cc_final: 0.8667 (tpp)
REVERT: A  240 MET cc_start: 0.8380 (tpp) cc_final: 0.7981 (tpp)
REVERT: A  257 MET cc_start: 0.9393 (tpp) cc_final: 0.9184 (tpp)
REVERT: A  395 LYS cc_start: 0.8398 (mttt) cc_final: 0.7994 (mtmm)
REVERT: A  443 LYS cc_start: 0.9606 (mttt) cc_final: 0.9352 (mtmm)
REVERT: A  485 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8144 (pp)
REVERT: A  494 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8808 (pt)
REVERT: A  531 MET cc_start: 0.9021 (pmm) cc_final: 0.8765 (pmm)
REVERT: A  541 MET cc_start: 0.9775 (mmm) cc_final: 0.9493 (mmm)
REVERT: B  100 MET cc_start: 0.9077 (mmm) cc_final: 0.8679 (tpp)
REVERT: B  240 MET cc_start: 0.8382 (tpp) cc_final: 0.7982 (tpp)
REVERT: B  257 MET cc_start: 0.9396 (tpp) cc_final: 0.9187 (tpp)
REVERT: B  395 LYS cc_start: 0.8396 (mttt) cc_final: 0.7995 (mtmm)
REVERT: B  443 LYS cc_start: 0.9605 (mttt) cc_final: 0.9355 (mtmm)
REVERT: B  485 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8474 (pp)
REVERT: B  494 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8794 (pt)
REVERT: B  531 MET cc_start: 0.9027 (pmm) cc_final: 0.8770 (pmm)
REVERT: B  541 MET cc_start: 0.9775 (mmm) cc_final: 0.9494 (mmm)
REVERT: C  100 MET cc_start: 0.9207 (mmm) cc_final: 0.8879 (mmm)
REVERT: C  240 MET cc_start: 0.8339 (tpp) cc_final: 0.7952 (tpp)
REVERT: C  257 MET cc_start: 0.9395 (tpp) cc_final: 0.9182 (tpp)
REVERT: C  395 LYS cc_start: 0.8392 (mttt) cc_final: 0.7990 (mtmm)
REVERT: C  443 LYS cc_start: 0.9606 (mttt) cc_final: 0.9352 (mtmm)
REVERT: C  485 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8476 (pp)
REVERT: C  494 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8799 (pt)
REVERT: C  531 MET cc_start: 0.9030 (pmm) cc_final: 0.8775 (pmm)
REVERT: C  541 MET cc_start: 0.9773 (mmm) cc_final: 0.9491 (mmm)
REVERT: D  100 MET cc_start: 0.9067 (mmm) cc_final: 0.8675 (tpp)
REVERT: D  240 MET cc_start: 0.8369 (tpp) cc_final: 0.7967 (tpp)
REVERT: D  257 MET cc_start: 0.9404 (tpp) cc_final: 0.9194 (tpp)
REVERT: D  395 LYS cc_start: 0.8397 (mttt) cc_final: 0.8000 (mtmm)
REVERT: D  443 LYS cc_start: 0.9603 (mttt) cc_final: 0.9349 (mtmm)
REVERT: D  485 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8474 (pp)
REVERT: D  494 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8798 (pt)
REVERT: D  531 MET cc_start: 0.9026 (pmm) cc_final: 0.8771 (pmm)
REVERT: D  541 MET cc_start: 0.9773 (mmm) cc_final: 0.9492 (mmm)
  outliers start: 16
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1306
  time to fit residues: 23.0999
Evaluate side-chains
  116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  494 ILE
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  494 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 187 optimal weight:    6.9990
   chunk 149 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 138 optimal weight:   10.0000
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.063987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046569 restraints weight = 64684.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 3.90
r_work: 0.2733 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  15124  Z= 0.123
  Angle     :  0.527   8.058  20613  Z= 0.269
  Chirality :  0.037   0.116   2378
  Planarity :  0.003   0.043   2543
  Dihedral  : 12.509 168.923   2103
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.49 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.20), residues: 1863
  helix:  2.79 (0.14), residues: 1296
  sheet:  2.75 (0.72), residues: 48
  loop : -0.45 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 420 
 TYR   0.009   0.001   TYR C  95 
 PHE   0.009   0.001   PHE B 270 
 TRP   0.012   0.001   TRP B 264 
 HIS   0.002   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (15124)
  covalent geometry    : angle       0.52653 (20613)
  hydrogen bonds       : bond        0.03208 (  970)
  hydrogen bonds       : angle       3.23028 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9059 (mmm) cc_final: 0.8649 (tpp)
REVERT: A  240 MET cc_start: 0.8619 (tpp) cc_final: 0.8257 (tpp)
REVERT: A  257 MET cc_start: 0.9374 (tpp) cc_final: 0.9161 (tpp)
REVERT: A  365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9187 (tttt)
REVERT: A  395 LYS cc_start: 0.8350 (mttt) cc_final: 0.7969 (mtmm)
REVERT: A  443 LYS cc_start: 0.9596 (mttt) cc_final: 0.9346 (mtmm)
REVERT: A  485 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8149 (pp)
REVERT: A  494 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8758 (pt)
REVERT: A  541 MET cc_start: 0.9773 (mmm) cc_final: 0.9486 (mmm)
REVERT: B  100 MET cc_start: 0.9069 (mmm) cc_final: 0.8657 (tpp)
REVERT: B  240 MET cc_start: 0.8619 (tpp) cc_final: 0.8258 (tpp)
REVERT: B  257 MET cc_start: 0.9369 (tpp) cc_final: 0.9153 (tpp)
REVERT: B  365 LYS cc_start: 0.9397 (tttt) cc_final: 0.9181 (tttt)
REVERT: B  395 LYS cc_start: 0.8345 (mttt) cc_final: 0.7965 (mtmm)
REVERT: B  443 LYS cc_start: 0.9593 (mttt) cc_final: 0.9346 (mtmm)
REVERT: B  485 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8450 (pp)
REVERT: B  494 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8850 (pt)
REVERT: B  541 MET cc_start: 0.9772 (mmm) cc_final: 0.9487 (mmm)
REVERT: C  100 MET cc_start: 0.9193 (mmm) cc_final: 0.8855 (mmm)
REVERT: C  240 MET cc_start: 0.8597 (tpp) cc_final: 0.8242 (tpp)
REVERT: C  257 MET cc_start: 0.9377 (tpp) cc_final: 0.9162 (tpp)
REVERT: C  365 LYS cc_start: 0.9401 (tttt) cc_final: 0.9188 (tttt)
REVERT: C  395 LYS cc_start: 0.8352 (mttt) cc_final: 0.7971 (mtmm)
REVERT: C  443 LYS cc_start: 0.9597 (mttt) cc_final: 0.9347 (mtmm)
REVERT: C  485 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8445 (pp)
REVERT: C  494 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (pt)
REVERT: C  541 MET cc_start: 0.9769 (mmm) cc_final: 0.9482 (mmm)
REVERT: D  100 MET cc_start: 0.9060 (mmm) cc_final: 0.8655 (tpp)
REVERT: D  240 MET cc_start: 0.8602 (tpp) cc_final: 0.8249 (tpp)
REVERT: D  257 MET cc_start: 0.9380 (tpp) cc_final: 0.9165 (tpp)
REVERT: D  365 LYS cc_start: 0.9402 (tttt) cc_final: 0.9188 (tttt)
REVERT: D  395 LYS cc_start: 0.8347 (mttt) cc_final: 0.7970 (mtmm)
REVERT: D  443 LYS cc_start: 0.9594 (mttt) cc_final: 0.9343 (mtmm)
REVERT: D  485 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8447 (pp)
REVERT: D  494 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (pt)
REVERT: D  541 MET cc_start: 0.9772 (mmm) cc_final: 0.9486 (mmm)
  outliers start: 16
  outliers final: 4
  residues processed: 122
  average time/residue: 0.1297
  time to fit residues: 23.6074
Evaluate side-chains
  112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  494 ILE
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  494 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 163 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0050
   chunk 49 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 151 optimal weight:    8.9990
   chunk 123 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    3.3800

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.062640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.045200 restraints weight = 65614.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 3.91
r_work: 0.2692 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15124  Z= 0.167
  Angle     :  0.574   8.713  20613  Z= 0.292
  Chirality :  0.039   0.118   2378
  Planarity :  0.003   0.043   2543
  Dihedral  : 12.476 168.645   2103
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  5.49 %
    Favored  : 93.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.00 (0.20), residues: 1863
  helix:  2.84 (0.14), residues: 1296
  sheet:  2.71 (0.72), residues: 48
  loop : -0.37 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 420 
 TYR   0.012   0.001   TYR A 511 
 PHE   0.010   0.001   PHE C 270 
 TRP   0.009   0.001   TRP C 264 
 HIS   0.003   0.001   HIS D 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (15124)
  covalent geometry    : angle       0.57435 (20613)
  hydrogen bonds       : bond        0.03655 (  970)
  hydrogen bonds       : angle       3.34990 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  100 MET cc_start: 0.9101 (mmm) cc_final: 0.8688 (tpp)
REVERT: A  168 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8630 (t80)
REVERT: A  240 MET cc_start: 0.8618 (tpp) cc_final: 0.8219 (tpp)
REVERT: A  257 MET cc_start: 0.9407 (tpp) cc_final: 0.9196 (tpp)
REVERT: A  395 LYS cc_start: 0.8515 (mttt) cc_final: 0.8093 (mtmm)
REVERT: A  426 MET cc_start: 0.8548 (mmm) cc_final: 0.8346 (tpp)
REVERT: A  443 LYS cc_start: 0.9629 (mttt) cc_final: 0.9358 (mtmm)
REVERT: A  485 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8241 (pp)
REVERT: A  494 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8962 (pt)
REVERT: A  541 MET cc_start: 0.9778 (mmm) cc_final: 0.9495 (mmm)
REVERT: B  100 MET cc_start: 0.9105 (mmm) cc_final: 0.8690 (tpp)
REVERT: B  168 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (t80)
REVERT: B  240 MET cc_start: 0.8622 (tpp) cc_final: 0.8223 (tpp)
REVERT: B  257 MET cc_start: 0.9411 (tpp) cc_final: 0.9197 (tpp)
REVERT: B  395 LYS cc_start: 0.8505 (mttt) cc_final: 0.8086 (mtmm)
REVERT: B  443 LYS cc_start: 0.9630 (mttt) cc_final: 0.9360 (mtmm)
REVERT: B  485 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8475 (pp)
REVERT: B  494 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8949 (pt)
REVERT: B  541 MET cc_start: 0.9781 (mmm) cc_final: 0.9498 (mmm)
REVERT: C  100 MET cc_start: 0.9253 (mmm) cc_final: 0.8896 (mmm)
REVERT: C  168 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (t80)
REVERT: C  240 MET cc_start: 0.8582 (tpp) cc_final: 0.8174 (tpp)
REVERT: C  257 MET cc_start: 0.9408 (tpp) cc_final: 0.9197 (tpp)
REVERT: C  365 LYS cc_start: 0.9447 (tttt) cc_final: 0.9207 (tttt)
REVERT: C  395 LYS cc_start: 0.8506 (mttt) cc_final: 0.8091 (mtmm)
REVERT: C  443 LYS cc_start: 0.9633 (mttt) cc_final: 0.9362 (mtmm)
REVERT: C  485 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: C  494 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8952 (pt)
REVERT: C  541 MET cc_start: 0.9777 (mmm) cc_final: 0.9492 (mmm)
REVERT: D  100 MET cc_start: 0.9099 (mmm) cc_final: 0.8690 (tpp)
REVERT: D  168 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8637 (t80)
REVERT: D  240 MET cc_start: 0.8591 (tpp) cc_final: 0.8189 (tpp)
REVERT: D  257 MET cc_start: 0.9411 (tpp) cc_final: 0.9203 (tpp)
REVERT: D  395 LYS cc_start: 0.8501 (mttt) cc_final: 0.8086 (mtmm)
REVERT: D  443 LYS cc_start: 0.9630 (mttt) cc_final: 0.9357 (mtmm)
REVERT: D  485 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8470 (pp)
REVERT: D  494 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8952 (pt)
REVERT: D  541 MET cc_start: 0.9779 (mmm) cc_final: 0.9493 (mmm)
  outliers start: 20
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1289
  time to fit residues: 24.3217
Evaluate side-chains
  126 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  168 TYR
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  494 ILE
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  168 TYR
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  494 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 148 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 89 optimal weight:    8.9990
   chunk 156 optimal weight:    4.9990
   chunk 95 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 130 optimal weight:    8.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.062847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.045412 restraints weight = 65297.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.91
r_work: 0.2698 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  15124  Z= 0.161
  Angle     :  0.586   9.068  20613  Z= 0.294
  Chirality :  0.039   0.144   2378
  Planarity :  0.003   0.043   2543
  Dihedral  : 12.475 169.198   2103
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  5.69 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.20), residues: 1863
  helix:  2.84 (0.14), residues: 1296
  sheet:  2.66 (0.73), residues: 48
  loop : -0.22 (0.29), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 420 
 TYR   0.010   0.001   TYR B  95 
 PHE   0.009   0.001   PHE A 270 
 TRP   0.010   0.001   TRP B 264 
 HIS   0.003   0.001   HIS D 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (15124)
  covalent geometry    : angle       0.58614 (20613)
  hydrogen bonds       : bond        0.03568 (  970)
  hydrogen bonds       : angle       3.33276 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  100 MET cc_start: 0.9072 (mmm) cc_final: 0.8653 (tpp)
REVERT: A  168 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8615 (t80)
REVERT: A  240 MET cc_start: 0.8672 (tpp) cc_final: 0.8270 (tpp)
REVERT: A  257 MET cc_start: 0.9392 (tpp) cc_final: 0.9186 (tpp)
REVERT: A  365 LYS cc_start: 0.9423 (tttt) cc_final: 0.9214 (tttt)
REVERT: A  395 LYS cc_start: 0.8492 (mttt) cc_final: 0.8082 (mtmm)
REVERT: A  426 MET cc_start: 0.8570 (mmm) cc_final: 0.8349 (tpp)
REVERT: A  443 LYS cc_start: 0.9617 (mttt) cc_final: 0.9341 (mtmm)
REVERT: A  485 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8336 (pp)
REVERT: A  494 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (pt)
REVERT: A  541 MET cc_start: 0.9780 (mmm) cc_final: 0.9497 (mmm)
REVERT: B  100 MET cc_start: 0.9076 (mmm) cc_final: 0.8658 (tpp)
REVERT: B  168 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8613 (t80)
REVERT: B  240 MET cc_start: 0.8674 (tpp) cc_final: 0.8274 (tpp)
REVERT: B  257 MET cc_start: 0.9390 (tpp) cc_final: 0.9181 (tpp)
REVERT: B  365 LYS cc_start: 0.9420 (tttt) cc_final: 0.9207 (tttt)
REVERT: B  395 LYS cc_start: 0.8476 (mttt) cc_final: 0.8069 (mtmm)
REVERT: B  443 LYS cc_start: 0.9619 (mttt) cc_final: 0.9347 (mtmm)
REVERT: B  485 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8481 (pp)
REVERT: B  494 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8969 (pt)
REVERT: B  541 MET cc_start: 0.9784 (mmm) cc_final: 0.9502 (mmm)
REVERT: C  100 MET cc_start: 0.9240 (mmm) cc_final: 0.8870 (mmm)
REVERT: C  168 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8624 (t80)
REVERT: C  240 MET cc_start: 0.8647 (tpp) cc_final: 0.8237 (tpp)
REVERT: C  257 MET cc_start: 0.9396 (tpp) cc_final: 0.9188 (tpp)
REVERT: C  395 LYS cc_start: 0.8482 (mttt) cc_final: 0.8074 (mtmm)
REVERT: C  443 LYS cc_start: 0.9620 (mttt) cc_final: 0.9344 (mtmm)
REVERT: C  485 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: C  494 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8970 (pt)
REVERT: C  541 MET cc_start: 0.9779 (mmm) cc_final: 0.9495 (mmm)
REVERT: D  100 MET cc_start: 0.9068 (mmm) cc_final: 0.8652 (tpp)
REVERT: D  168 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8620 (t80)
REVERT: D  240 MET cc_start: 0.8652 (tpp) cc_final: 0.8248 (tpp)
REVERT: D  257 MET cc_start: 0.9401 (tpp) cc_final: 0.9197 (tpp)
REVERT: D  365 LYS cc_start: 0.9431 (tttt) cc_final: 0.9219 (tttt)
REVERT: D  395 LYS cc_start: 0.8479 (mttt) cc_final: 0.8073 (mtmm)
REVERT: D  443 LYS cc_start: 0.9621 (mttt) cc_final: 0.9348 (mtmm)
REVERT: D  485 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: D  494 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8973 (pt)
REVERT: D  541 MET cc_start: 0.9780 (mmm) cc_final: 0.9495 (mmm)
  outliers start: 20
  outliers final: 8
  residues processed: 124
  average time/residue: 0.1327
  time to fit residues: 24.5525
Evaluate side-chains
  126 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  234 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  168 TYR
Chi-restraints excluded: chain C residue  234 TRP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  494 ILE
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  168 TYR
Chi-restraints excluded: chain D residue  234 TRP
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  494 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 170 optimal weight:    6.9990
   chunk 133 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 181 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 127 optimal weight:   10.0000
   chunk 145 optimal weight:   10.0000
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.064993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.047638 restraints weight = 64543.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 3.91
r_work: 0.2760 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15124  Z= 0.106
  Angle     :  0.550   9.488  20613  Z= 0.272
  Chirality :  0.038   0.119   2378
  Planarity :  0.003   0.044   2543
  Dihedral  : 12.486 169.979   2103
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.51 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.15 (0.20), residues: 1863
  helix:  2.90 (0.14), residues: 1300
  sheet:  2.75 (0.73), residues: 48
  loop : -0.17 (0.29), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 420 
 TYR   0.009   0.001   TYR A 364 
 PHE   0.010   0.001   PHE A 270 
 TRP   0.015   0.001   TRP C 264 
 HIS   0.002   0.000   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (15124)
  covalent geometry    : angle       0.55034 (20613)
  hydrogen bonds       : bond        0.02793 (  970)
  hydrogen bonds       : angle       3.14724 ( 2853)

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

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

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3726 Ramachandran restraints generated.
    1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9049 (mmm) cc_final: 0.8618 (tpp)
REVERT: A  240 MET cc_start: 0.8645 (tpp) cc_final: 0.8244 (tpp)
REVERT: A  257 MET cc_start: 0.9330 (tpp) cc_final: 0.9117 (tpp)
REVERT: A  395 LYS cc_start: 0.8367 (mttt) cc_final: 0.7991 (mtmm)
REVERT: A  426 MET cc_start: 0.8451 (mmm) cc_final: 0.8229 (tpp)
REVERT: A  485 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8312 (pp)
REVERT: A  541 MET cc_start: 0.9773 (mmm) cc_final: 0.9482 (mmm)
REVERT: B  100 MET cc_start: 0.9055 (mmm) cc_final: 0.8627 (tpp)
REVERT: B  240 MET cc_start: 0.8644 (tpp) cc_final: 0.8248 (tpp)
REVERT: B  257 MET cc_start: 0.9319 (tpp) cc_final: 0.9103 (tpp)
REVERT: B  395 LYS cc_start: 0.8350 (mttt) cc_final: 0.7978 (mtmm)
REVERT: B  485 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8488 (pp)
REVERT: B  541 MET cc_start: 0.9781 (mmm) cc_final: 0.9494 (mmm)
REVERT: C  100 MET cc_start: 0.9172 (mmm) cc_final: 0.8804 (mmm)
REVERT: C  240 MET cc_start: 0.8612 (tpp) cc_final: 0.8201 (tpp)
REVERT: C  257 MET cc_start: 0.9326 (tpp) cc_final: 0.9110 (tpp)
REVERT: C  395 LYS cc_start: 0.8362 (mttt) cc_final: 0.7983 (mtmm)
REVERT: C  485 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8486 (pp)
REVERT: C  541 MET cc_start: 0.9774 (mmm) cc_final: 0.9483 (mmm)
REVERT: D  100 MET cc_start: 0.9044 (mmm) cc_final: 0.8622 (tpp)
REVERT: D  240 MET cc_start: 0.8623 (tpp) cc_final: 0.8218 (tpp)
REVERT: D  257 MET cc_start: 0.9337 (tpp) cc_final: 0.9123 (tpp)
REVERT: D  395 LYS cc_start: 0.8342 (mttt) cc_final: 0.8047 (mtmm)
REVERT: D  485 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: D  541 MET cc_start: 0.9774 (mmm) cc_final: 0.9483 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 124
  average time/residue: 0.1335
  time to fit residues: 24.4293
Evaluate side-chains
  113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 120 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 185 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 125 optimal weight:   10.0000
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.062350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.044922 restraints weight = 64922.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 3.91
r_work: 0.2683 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15124  Z= 0.197
  Angle     :  0.616  10.012  20613  Z= 0.309
  Chirality :  0.040   0.136   2378
  Planarity :  0.003   0.042   2543
  Dihedral  : 12.462 168.323   2103
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  6.92 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.19 (0.20), residues: 1863
  helix:  2.93 (0.14), residues: 1296
  sheet:  2.17 (0.66), residues: 60
  loop : -0.15 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 534 
 TYR   0.013   0.001   TYR A 511 
 PHE   0.009   0.001   PHE A 252 
 TRP   0.010   0.001   TRP C 172 
 HIS   0.004   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (15124)
  covalent geometry    : angle       0.61578 (20613)
  hydrogen bonds       : bond        0.03782 (  970)
  hydrogen bonds       : angle       3.39212 ( 2853)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3472.44 seconds
wall clock time: 60 minutes 33.41 seconds (3633.41 seconds total)