Starting phenix.real_space_refine
on Mon Aug 25 02:06:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tz7_41736/08_2025/8tz7_41736_trim.cif"
  }
  resolution = 3.0
  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=   0.002 sd=   0.083
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      87      5.16       5
     C    8187      2.51       5
     N    1923      2.21       5
     O    2139      1.98       5
     H   12069      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 24408
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8076
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 8076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8076
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "C"
      Number of atoms: 8076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8076
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'LBN': 1, 'XMO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 15
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'LBN': 1, 'XMO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 15
    Chain: "C"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'LBN': 1, 'XMO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 15
  Time building chain proxies: 4.69, per 1000 atoms: 0.19
  Number of scatterers: 24408
  At special positions: 0
  Unit cell: (128.52, 128.52, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      87     16.00
     P       3     15.00
     O    2139      8.00
     N    1923      7.00
     C    8187      6.00
     H   12069      1.00
    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: 2.33
  Conformation dependent library (CDL) restraints added in 772.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2946

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 0 sheets defined
      89.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 130
      removed outlier: 5.832A  pdb=" N   THR A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   THR A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 157 through 203
      Proline residue:  A 167  - end of helix
      removed outlier: 4.714A  pdb=" N   PHE A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   TRP A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   TRP A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A 182 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 223
      removed outlier: 3.760A  pdb=" N   LEU A 207 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A 209 " --> pdb=" O   GLN A 205 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE A 210 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 252
      removed outlier: 4.442A  pdb=" N   VAL A 235 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 277
      removed outlier: 3.513A  pdb=" N   ALA A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 4.404A  pdb=" N   THR A 286 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 293
    Processing helix  chain 'A' and resid 294 through 312
      removed outlier: 3.831A  pdb=" N   VAL A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 330
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 349 through 361
      Proline residue:  A 356  - end of helix
      Proline residue:  A 359  - end of helix
    Processing helix  chain 'A' and resid 362 through 376
      removed outlier: 3.637A  pdb=" N   THR A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 4.058A  pdb=" N   GLY A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ALA A 384 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A 389 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 414
      removed outlier: 4.083A  pdb=" N   ALA A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 423 through 429
    Processing helix  chain 'A' and resid 437 through 481
      removed outlier: 3.706A  pdb=" N   SER A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   SER A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET A 480 " --> pdb=" O   TRP A 476 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   PHE A 481 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.590A  pdb=" N   TYR A 494 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 503
    Processing helix  chain 'A' and resid 506 through 523
      removed outlier: 4.274A  pdb=" N   PHE A 511 " --> pdb=" O   TRP A 507 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   MET A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 516 " --> pdb=" O   MET A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 542
      removed outlier: 3.988A  pdb=" N   ALA A 528 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 566
    Processing helix  chain 'A' and resid 571 through 573
      No H-bonds generated for 'chain 'A' and resid 571 through 573'
    Processing helix  chain 'A' and resid 574 through 586
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 596 through 619
      removed outlier: 3.548A  pdb=" N   LEU A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A 602 " --> pdb=" O   MET A 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 130
      removed outlier: 5.832A  pdb=" N   THR B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   THR B 106 " --> pdb=" O   GLU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 157
    Processing helix  chain 'B' and resid 157 through 203
      Proline residue:  B 167  - end of helix
      removed outlier: 4.714A  pdb=" N   PHE B 177 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   TRP B 178 " --> pdb=" O   SER B 174 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   TRP B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 223
      removed outlier: 3.761A  pdb=" N   LEU B 207 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER B 209 " --> pdb=" O   GLN B 205 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE B 210 " --> pdb=" O   GLN B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 252
      removed outlier: 4.441A  pdb=" N   VAL B 235 " --> pdb=" O   TYR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 277
      removed outlier: 3.514A  pdb=" N   ALA B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   PHE B 259 " --> pdb=" O   GLY B 255 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP B 260 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 282
    Processing helix  chain 'B' and resid 283 through 287
      removed outlier: 4.403A  pdb=" N   THR B 286 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 293
    Processing helix  chain 'B' and resid 294 through 312
      removed outlier: 3.832A  pdb=" N   VAL B 298 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE B 299 " --> pdb=" O   LEU B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 330
    Processing helix  chain 'B' and resid 332 through 342
    Processing helix  chain 'B' and resid 349 through 361
      Proline residue:  B 356  - end of helix
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 362 through 376
      removed outlier: 3.637A  pdb=" N   THR B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
      removed outlier: 4.059A  pdb=" N   GLY B 383 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ALA B 384 " --> pdb=" O   SER B 380 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY B 389 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 414
      removed outlier: 4.083A  pdb=" N   ALA B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      Proline residue:  B 404  - end of helix
    Processing helix  chain 'B' and resid 423 through 429
    Processing helix  chain 'B' and resid 437 through 481
      removed outlier: 3.706A  pdb=" N   SER B 449 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 446 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   SER B 451 " --> pdb=" O   SER B 447 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU B 452 " --> pdb=" O   SER B 448 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET B 480 " --> pdb=" O   TRP B 476 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   PHE B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 496
      removed outlier: 3.589A  pdb=" N   TYR B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 503
    Processing helix  chain 'B' and resid 506 through 523
      removed outlier: 4.274A  pdb=" N   PHE B 511 " --> pdb=" O   TRP B 507 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   MET B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 516 " --> pdb=" O   MET B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 542
      removed outlier: 3.988A  pdb=" N   ALA B 528 " --> pdb=" O   ASN B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 566
    Processing helix  chain 'B' and resid 571 through 573
      No H-bonds generated for 'chain 'B' and resid 571 through 573'
    Processing helix  chain 'B' and resid 574 through 586
    Processing helix  chain 'B' and resid 589 through 596
    Processing helix  chain 'B' and resid 596 through 619
      removed outlier: 3.548A  pdb=" N   LEU B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE B 602 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 130
      removed outlier: 5.833A  pdb=" N   THR C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   THR C 106 " --> pdb=" O   GLU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 157
    Processing helix  chain 'C' and resid 157 through 203
      Proline residue:  C 167  - end of helix
      removed outlier: 4.713A  pdb=" N   PHE C 177 " --> pdb=" O   ASP C 173 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   TRP C 178 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   TRP C 181 " --> pdb=" O   PHE C 177 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL C 182 " --> pdb=" O   TRP C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 223
      removed outlier: 3.761A  pdb=" N   LEU C 207 " --> pdb=" O   GLY C 203 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER C 209 " --> pdb=" O   GLN C 205 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE C 210 " --> pdb=" O   GLN C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 252
      removed outlier: 4.441A  pdb=" N   VAL C 235 " --> pdb=" O   TYR C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 277
      removed outlier: 3.513A  pdb=" N   ALA C 258 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   PHE C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP C 260 " --> pdb=" O   PHE C 256 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER C 273 " --> pdb=" O   PHE C 269 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP C 274 " --> pdb=" O   LEU C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 282
    Processing helix  chain 'C' and resid 283 through 287
      removed outlier: 4.404A  pdb=" N   THR C 286 " --> pdb=" O   GLU C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 293
    Processing helix  chain 'C' and resid 294 through 312
      removed outlier: 3.831A  pdb=" N   VAL C 298 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 330
    Processing helix  chain 'C' and resid 332 through 342
    Processing helix  chain 'C' and resid 349 through 361
      Proline residue:  C 356  - end of helix
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 362 through 376
      removed outlier: 3.636A  pdb=" N   THR C 376 " --> pdb=" O   ALA C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 389
      removed outlier: 4.059A  pdb=" N   GLY C 383 " --> pdb=" O   GLY C 379 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ALA C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY C 389 " --> pdb=" O   TYR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 414
      removed outlier: 4.084A  pdb=" N   ALA C 403 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      Proline residue:  C 404  - end of helix
    Processing helix  chain 'C' and resid 423 through 429
    Processing helix  chain 'C' and resid 437 through 481
      removed outlier: 3.706A  pdb=" N   SER C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE C 450 " --> pdb=" O   ALA C 446 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   SER C 451 " --> pdb=" O   SER C 447 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU C 452 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET C 480 " --> pdb=" O   TRP C 476 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   PHE C 481 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 496
      removed outlier: 3.590A  pdb=" N   TYR C 494 " --> pdb=" O   VAL C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 503
    Processing helix  chain 'C' and resid 506 through 523
      removed outlier: 4.274A  pdb=" N   PHE C 511 " --> pdb=" O   TRP C 507 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   MET C 512 " --> pdb=" O   GLN C 508 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU C 516 " --> pdb=" O   MET C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 542
      removed outlier: 3.988A  pdb=" N   ALA C 528 " --> pdb=" O   ASN C 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 566
    Processing helix  chain 'C' and resid 571 through 573
      No H-bonds generated for 'chain 'C' and resid 571 through 573'
    Processing helix  chain 'C' and resid 574 through 586
    Processing helix  chain 'C' and resid 589 through 596
    Processing helix  chain 'C' and resid 596 through 619
      removed outlier: 3.548A  pdb=" N   LEU C 601 " --> pdb=" O   ALA C 597 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE C 602 " --> pdb=" O   MET C 598 " (cutoff:3.500A)

    967 hydrogen bonds defined for protein.
    2856 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: 4.96

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12051
        1.03 -     1.23: 31
        1.23 -     1.42: 5345
        1.42 -     1.62: 7149
        1.62 -     1.81: 165
  Bond restraints: 24741
  Sorted by residual:
  bond pdb=" C11 XMO B 801 "
       pdb=" O12 XMO B 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.683 -0.285 2.00e-02 2.50e+03 2.02e+02
  bond pdb=" C11 XMO A 801 "
       pdb=" O12 XMO A 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.682 -0.284 2.00e-02 2.50e+03 2.01e+02
  bond pdb=" C11 XMO C 801 "
       pdb=" O12 XMO C 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.681 -0.283 2.00e-02 2.50e+03 2.01e+02
  bond pdb=" C10 XMO B 801 "
       pdb=" C11 XMO B 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.291  0.243 2.00e-02 2.50e+03 1.48e+02
  bond pdb=" C10 XMO A 801 "
       pdb=" C11 XMO A 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.291  0.243 2.00e-02 2.50e+03 1.47e+02
  ... (remaining 24736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 44413
        3.18 -     6.35: 129
        6.35 -     9.53: 11
        9.53 -    12.71: 3
       12.71 -    15.89: 3
  Bond angle restraints: 44559
  Sorted by residual:
  angle pdb=" O1  LBN C 802 "
        pdb=" P1  LBN C 802 "
        pdb=" O2  LBN C 802 "
      ideal   model   delta    sigma   weight residual
      93.45  109.34  -15.89 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" O1  LBN B 802 "
        pdb=" P1  LBN B 802 "
        pdb=" O2  LBN B 802 "
      ideal   model   delta    sigma   weight residual
      93.45  109.32  -15.87 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" O1  LBN A 802 "
        pdb=" P1  LBN A 802 "
        pdb=" O2  LBN A 802 "
      ideal   model   delta    sigma   weight residual
      93.45  109.30  -15.85 3.00e+00 1.11e-01 2.79e+01
  angle pdb=" N   ASP A 548 "
        pdb=" CA  ASP A 548 "
        pdb=" C   ASP A 548 "
      ideal   model   delta    sigma   weight residual
     108.19  103.85    4.34 1.29e+00 6.01e-01 1.13e+01
  angle pdb=" N   ASP B 548 "
        pdb=" CA  ASP B 548 "
        pdb=" C   ASP B 548 "
      ideal   model   delta    sigma   weight residual
     108.19  103.89    4.30 1.29e+00 6.01e-01 1.11e+01
  ... (remaining 44554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.60: 11314
       26.60 -    53.21: 406
       53.21 -    79.81: 106
       79.81 -   106.41: 6
      106.41 -   133.02: 3
  Dihedral angle restraints: 11835
    sinusoidal: 6105
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" O5  LBN A 802 "
           pdb=" C2  LBN A 802 "
           pdb=" C3  LBN A 802 "
           pdb=" O7  LBN A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -164.31 -133.02     1      3.00e+01 1.11e-03 1.79e+01
  dihedral pdb=" O5  LBN C 802 "
           pdb=" C2  LBN C 802 "
           pdb=" C3  LBN C 802 "
           pdb=" O7  LBN C 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -164.35 -132.98     1      3.00e+01 1.11e-03 1.79e+01
  dihedral pdb=" O5  LBN B 802 "
           pdb=" C2  LBN B 802 "
           pdb=" C3  LBN B 802 "
           pdb=" O7  LBN B 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -164.36 -132.97     1      3.00e+01 1.11e-03 1.79e+01
  ... (remaining 11832 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1756
       0.067 -    0.134: 230
       0.134 -    0.202: 0
       0.202 -    0.269: 0
       0.269 -    0.336: 3
  Chirality restraints: 1989
  Sorted by residual:
  chirality pdb=" C10 XMO B 801 "
            pdb=" C09 XMO B 801 "
            pdb=" C11 XMO B 801 "
            pdb=" O22 XMO B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.40    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" C10 XMO C 801 "
            pdb=" C09 XMO C 801 "
            pdb=" C11 XMO C 801 "
            pdb=" O22 XMO C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.40    0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" C10 XMO A 801 "
            pdb=" C09 XMO A 801 "
            pdb=" C11 XMO A 801 "
            pdb=" O22 XMO A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.41    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 1986 not shown)

  Planarity restraints: 3633
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 295 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.05e+00
        pdb=" N   PRO C 296 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 296 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 296 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 295 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.02e+00
        pdb=" N   PRO A 296 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 296 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 296 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 295 "    0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO B 296 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "    0.024 5.00e-02 4.00e+02
  ... (remaining 3630 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 486
        2.13 -     2.75: 42845
        2.75 -     3.36: 69920
        3.36 -     3.98: 86051
        3.98 -     4.60: 139144
  Nonbonded interactions: 338446
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 248 "
            pdb=" HG1 THR A 252 "
     model   vdw
     1.511 2.450
  nonbonded pdb=" O   LEU B 248 "
            pdb=" HG1 THR B 252 "
     model   vdw
     1.513 2.450
  nonbonded pdb=" O   LEU C 248 "
            pdb=" HG1 THR C 252 "
     model   vdw
     1.513 2.450
  nonbonded pdb=" O   LEU C 195 "
            pdb=" HG1 THR C 199 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" O   LEU B 195 "
            pdb=" HG1 THR B 199 "
     model   vdw
     1.560 2.450
  ... (remaining 338441 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:             0.160
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     23.180
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  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:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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      :  0.010   0.285  12672  Z= 0.487
  Angle     :  0.682  15.886  17241  Z= 0.330
  Chirality :  0.040   0.336   1989
  Planarity :  0.003   0.044   2091
  Dihedral  : 12.773 133.018   4365
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.12 %
    Favored  : 96.39 %
  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 aren not related in a simple way.
  whole:  3.50 (0.21), residues: 1593
  helix:  2.94 (0.14), residues: 1296
  sheet:  None (None), residues: 0
  loop : -0.75 (0.30), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 539 
 TYR   0.007   0.001   TYR B 519 
 PHE   0.015   0.001   PHE B 488 
 TRP   0.010   0.001   TRP A 316 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00978 (12672)
  covalent geometry    : angle       0.68238 (17241)
  hydrogen bonds       : bond        0.14689 (  967)
  hydrogen bonds       : angle       5.14034 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  241 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 235
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6891 (tp) cc_final: 0.6669 (mt)
REVERT: A  307 MET cc_start: 0.8471 (mtm) cc_final: 0.8098 (mtp)
REVERT: A  497 MET cc_start: 0.7792 (tmt) cc_final: 0.6777 (tmt)
REVERT: A  598 MET cc_start: 0.8202 (tpp) cc_final: 0.7635 (tpt)
REVERT: B  307 MET cc_start: 0.8419 (mtm) cc_final: 0.8215 (mtp)
REVERT: B  329 MET cc_start: 0.8462 (mtp) cc_final: 0.8238 (mtm)
REVERT: C  329 MET cc_start: 0.8538 (mtp) cc_final: 0.8160 (mtm)
REVERT: C  344 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p90)
REVERT: C  430 MET cc_start: 0.8057 (mtt) cc_final: 0.7540 (mtt)
REVERT: C  497 MET cc_start: 0.7517 (tmt) cc_final: 0.7170 (tmt)
  outliers start: 6
  outliers final: 2
  residues processed: 239
  average time/residue: 0.7085
  time to fit residues: 192.4695
Evaluate side-chains
  175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 172
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain C residue  344 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    1.5544

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

Flipped N/Q/H residues before XYZ refinement:
B 508 GLN
C 423 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.158041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.129403 restraints weight = 36458.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.24
r_work: 0.2938 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12672  Z= 0.180
  Angle     :  0.548   5.818  17241  Z= 0.296
  Chirality :  0.038   0.124   1989
  Planarity :  0.004   0.056   2091
  Dihedral  :  9.468 145.851   1860
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.94 %
    Favored  : 88.46 %
  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 aren not related in a simple way.
  whole:  2.73 (0.21), residues: 1593
  helix:  2.35 (0.14), residues: 1320
  sheet:  None (None), residues: 0
  loop : -1.05 (0.32), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 539 
 TYR   0.007   0.001   TYR A 309 
 PHE   0.018   0.002   PHE A 523 
 TRP   0.008   0.001   TRP C 323 
 HIS   0.005   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12672)
  covalent geometry    : angle       0.54830 (17241)
  hydrogen bonds       : bond        0.05893 (  967)
  hydrogen bonds       : angle       4.45807 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6964 (tp) cc_final: 0.6695 (mp)
REVERT: A  307 MET cc_start: 0.8616 (mtm) cc_final: 0.8294 (mtp)
REVERT: A  583 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8257 (t)
REVERT: A  598 MET cc_start: 0.8491 (tpp) cc_final: 0.7950 (tpt)
REVERT: B  205 GLN cc_start: 0.7844 (mp10) cc_final: 0.7266 (mt0)
REVERT: B  284 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7461 (mtpp)
REVERT: B  482 ASP cc_start: 0.8352 (t0) cc_final: 0.7981 (m-30)
REVERT: B  497 MET cc_start: 0.8261 (tmt) cc_final: 0.7531 (tmt)
REVERT: B  620 ASN cc_start: 0.8204 (p0) cc_final: 0.7927 (t0)
REVERT: C  129 MET cc_start: 0.7398 (mtp) cc_final: 0.7094 (mtp)
REVERT: C  329 MET cc_start: 0.8918 (mtp) cc_final: 0.8552 (mtm)
REVERT: C  344 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8159 (p90)
REVERT: C  470 MET cc_start: 0.8423 (ttm) cc_final: 0.8139 (ttm)
REVERT: C  497 MET cc_start: 0.8205 (tmt) cc_final: 0.7304 (tmt)
REVERT: C  583 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8216 (t)
  outliers start: 20
  outliers final: 8
  residues processed: 193
  average time/residue: 0.8026
  time to fit residues: 174.7667
Evaluate side-chains
  167 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain C residue  344 PHE
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  583 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:   40.0000
   chunk 12 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
B 315 GLN
B 508 GLN
C 508 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.156407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.122912 restraints weight = 36627.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.26
r_work: 0.2897 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12672  Z= 0.150
  Angle     :  0.476   4.448  17241  Z= 0.256
  Chirality :  0.035   0.115   1989
  Planarity :  0.004   0.054   2091
  Dihedral  :  8.787 142.050   1860
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.38 %
    Favored  : 84.94 %
  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 aren not related in a simple way.
  whole:  2.84 (0.21), residues: 1593
  helix:  2.45 (0.14), residues: 1329
  sheet:  None (None), residues: 0
  loop : -1.22 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 557 
 TYR   0.008   0.001   TYR C 494 
 PHE   0.014   0.001   PHE B 413 
 TRP   0.009   0.001   TRP C 323 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12672)
  covalent geometry    : angle       0.47566 (17241)
  hydrogen bonds       : bond        0.05621 (  967)
  hydrogen bonds       : angle       4.20979 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  248 LEU cc_start: 0.6857 (tp) cc_final: 0.6540 (mp)
REVERT: A  307 MET cc_start: 0.8513 (mtm) cc_final: 0.8214 (mtp)
REVERT: A  485 GLN cc_start: 0.8286 (mp10) cc_final: 0.8019 (mp10)
REVERT: A  497 MET cc_start: 0.8227 (tmt) cc_final: 0.7195 (tmt)
REVERT: A  502 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7473 (mmp)
REVERT: A  598 MET cc_start: 0.8527 (tpp) cc_final: 0.8004 (tpt)
REVERT: A  620 ASN cc_start: 0.7848 (p0) cc_final: 0.7540 (t0)
REVERT: B  205 GLN cc_start: 0.7840 (mp10) cc_final: 0.7144 (mt0)
REVERT: B  257 MET cc_start: 0.7485 (mmm) cc_final: 0.7156 (mtm)
REVERT: B  482 ASP cc_start: 0.8359 (t0) cc_final: 0.7972 (m-30)
REVERT: B  583 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (t)
REVERT: C  189 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7553 (tm)
REVERT: C  344 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8402 (p90)
REVERT: C  470 MET cc_start: 0.8429 (ttm) cc_final: 0.8177 (ttm)
  outliers start: 21
  outliers final: 12
  residues processed: 181
  average time/residue: 0.8197
  time to fit residues: 167.6621
Evaluate side-chains
  175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  344 PHE
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  443 THR
Chi-restraints excluded: chain C residue  577 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 128 optimal weight:    1.9990
   chunk 106 optimal weight:   20.0000
   chunk 81 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 135 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 394 HIS
A 508 GLN
B 394 HIS
B 508 GLN
C 508 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.138168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.100740 restraints weight = 37176.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.52
r_work: 0.2837 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12672  Z= 0.169
  Angle     :  0.490   4.518  17241  Z= 0.265
  Chirality :  0.036   0.115   1989
  Planarity :  0.004   0.057   2091
  Dihedral  :  8.633 144.150   1858
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.62 %
    Favored  : 84.13 %
  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 aren not related in a simple way.
  whole:  2.57 (0.21), residues: 1593
  helix:  2.25 (0.14), residues: 1335
  sheet:  None (None), residues: 0
  loop : -1.28 (0.31), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.008   0.001   TYR C 494 
 PHE   0.016   0.002   PHE B 413 
 TRP   0.008   0.001   TRP C 323 
 HIS   0.003   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12672)
  covalent geometry    : angle       0.49020 (17241)
  hydrogen bonds       : bond        0.05845 (  967)
  hydrogen bonds       : angle       4.24173 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  192 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6949 (tp) cc_final: 0.6580 (mp)
REVERT: A  307 MET cc_start: 0.8557 (mtm) cc_final: 0.8328 (mtp)
REVERT: A  344 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8260 (p90)
REVERT: A  477 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: A  497 MET cc_start: 0.8233 (tmt) cc_final: 0.7194 (tmt)
REVERT: A  598 MET cc_start: 0.8651 (tpp) cc_final: 0.8178 (tpt)
REVERT: B  189 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7597 (tt)
REVERT: B  205 GLN cc_start: 0.7836 (mp10) cc_final: 0.6987 (mt0)
REVERT: B  257 MET cc_start: 0.7481 (mmm) cc_final: 0.7122 (mtm)
REVERT: B  284 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7309 (mtpp)
REVERT: B  482 ASP cc_start: 0.8359 (t0) cc_final: 0.7895 (m-30)
REVERT: B  620 ASN cc_start: 0.8195 (p0) cc_final: 0.7878 (t0)
REVERT: C  189 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7562 (tm)
REVERT: C  329 MET cc_start: 0.8839 (mtp) cc_final: 0.8585 (mtm)
REVERT: C  344 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8494 (p90)
REVERT: C  418 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6655 (pt0)
REVERT: C  470 MET cc_start: 0.8419 (ttm) cc_final: 0.8164 (ttm)
REVERT: C  497 MET cc_start: 0.8156 (tmt) cc_final: 0.7088 (tmt)
REVERT: C  583 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (t)
  outliers start: 28
  outliers final: 10
  residues processed: 179
  average time/residue: 0.8481
  time to fit residues: 170.5706
Evaluate side-chains
  179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  344 PHE
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  443 THR
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0870
   chunk 156 optimal weight:    3.9990
   chunk 139 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 141 optimal weight:    4.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 508 GLN
B 508 GLN
C 508 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.133159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.096426 restraints weight = 37365.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.45
r_work: 0.2842 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12672  Z= 0.167
  Angle     :  0.485   4.509  17241  Z= 0.260
  Chirality :  0.036   0.112   1989
  Planarity :  0.004   0.056   2091
  Dihedral  :  8.510 143.764   1858
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.42 %
    Favored  : 83.89 %
  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 aren not related in a simple way.
  whole:  2.56 (0.21), residues: 1593
  helix:  2.26 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.20 (0.30), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.006   0.001   TYR C 494 
 PHE   0.014   0.001   PHE B 413 
 TRP   0.008   0.001   TRP A 323 
 HIS   0.003   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12672)
  covalent geometry    : angle       0.48529 (17241)
  hydrogen bonds       : bond        0.05785 (  967)
  hydrogen bonds       : angle       4.21734 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.7106 (tp) cc_final: 0.6738 (mp)
REVERT: A  307 MET cc_start: 0.8607 (mtm) cc_final: 0.8384 (mtp)
REVERT: A  344 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8308 (p90)
REVERT: A  497 MET cc_start: 0.8269 (tmt) cc_final: 0.7265 (tmt)
REVERT: A  598 MET cc_start: 0.8688 (tpp) cc_final: 0.8172 (tpt)
REVERT: B  205 GLN cc_start: 0.7901 (mp10) cc_final: 0.7131 (mt0)
REVERT: B  257 MET cc_start: 0.7637 (mmm) cc_final: 0.7324 (mtm)
REVERT: B  482 ASP cc_start: 0.8454 (t0) cc_final: 0.8019 (m-30)
REVERT: B  620 ASN cc_start: 0.8171 (p0) cc_final: 0.7818 (t0)
REVERT: C  189 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7689 (tm)
REVERT: C  329 MET cc_start: 0.8821 (mtp) cc_final: 0.8580 (mtm)
REVERT: C  470 MET cc_start: 0.8436 (ttm) cc_final: 0.8180 (ttm)
  outliers start: 21
  outliers final: 12
  residues processed: 176
  average time/residue: 0.8021
  time to fit residues: 158.9195
Evaluate side-chains
  174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  443 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  443 THR
Chi-restraints excluded: chain C residue  577 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 142 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 155 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 508 GLN
B 508 GLN
C 508 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.156343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.121766 restraints weight = 36538.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 1.38
r_work: 0.2940 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12672  Z= 0.117
  Angle     :  0.437   4.377  17241  Z= 0.232
  Chirality :  0.034   0.112   1989
  Planarity :  0.004   0.051   2091
  Dihedral  :  8.119 139.742   1856
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.06 %
    Favored  : 83.17 %
  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 aren not related in a simple way.
  whole:  2.90 (0.21), residues: 1593
  helix:  2.50 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.12 (0.30), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 557 
 TYR   0.004   0.001   TYR B 216 
 PHE   0.010   0.001   PHE C 413 
 TRP   0.009   0.001   TRP A 323 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12672)
  covalent geometry    : angle       0.43683 (17241)
  hydrogen bonds       : bond        0.04769 (  967)
  hydrogen bonds       : angle       4.03485 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6912 (tp) cc_final: 0.6569 (mp)
REVERT: A  307 MET cc_start: 0.8505 (mtm) cc_final: 0.8269 (mtp)
REVERT: A  344 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8293 (p90)
REVERT: A  485 GLN cc_start: 0.8255 (mp10) cc_final: 0.7982 (mt0)
REVERT: A  497 MET cc_start: 0.8282 (tmt) cc_final: 0.7256 (tmt)
REVERT: A  598 MET cc_start: 0.8710 (tpp) cc_final: 0.8221 (tpt)
REVERT: B  189 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (tt)
REVERT: B  205 GLN cc_start: 0.7848 (mp10) cc_final: 0.7083 (mt0)
REVERT: B  257 MET cc_start: 0.7426 (mmm) cc_final: 0.7181 (mtm)
REVERT: B  482 ASP cc_start: 0.8366 (t0) cc_final: 0.7945 (m-30)
REVERT: C  189 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7658 (tm)
REVERT: C  284 LYS cc_start: 0.8409 (mttm) cc_final: 0.8145 (mtpp)
REVERT: C  329 MET cc_start: 0.8810 (mtp) cc_final: 0.8576 (mtm)
REVERT: C  418 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6665 (pt0)
REVERT: C  470 MET cc_start: 0.8426 (ttm) cc_final: 0.8203 (ttm)
REVERT: C  583 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8173 (t)
  outliers start: 22
  outliers final: 8
  residues processed: 180
  average time/residue: 0.8783
  time to fit residues: 178.1020
Evaluate side-chains
  175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.155988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.125984 restraints weight = 36388.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.19
r_work: 0.2915 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12672  Z= 0.123
  Angle     :  0.443   4.406  17241  Z= 0.235
  Chirality :  0.034   0.111   1989
  Planarity :  0.004   0.050   2091
  Dihedral  :  8.058 139.329   1856
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.11 %
    Favored  : 82.37 %
  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 aren not related in a simple way.
  whole:  2.92 (0.21), residues: 1593
  helix:  2.52 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.10 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 133 
 TYR   0.004   0.001   TYR A 119 
 PHE   0.011   0.001   PHE C 413 
 TRP   0.008   0.001   TRP A 323 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12672)
  covalent geometry    : angle       0.44271 (17241)
  hydrogen bonds       : bond        0.04866 (  967)
  hydrogen bonds       : angle       4.01466 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.7021 (tp) cc_final: 0.6694 (mp)
REVERT: A  307 MET cc_start: 0.8508 (mtm) cc_final: 0.8287 (mtp)
REVERT: A  325 MET cc_start: 0.7921 (mtp) cc_final: 0.7712 (mtp)
REVERT: A  497 MET cc_start: 0.8316 (tmt) cc_final: 0.7283 (tmt)
REVERT: A  502 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7350 (mmp)
REVERT: A  598 MET cc_start: 0.8704 (tpp) cc_final: 0.8214 (tpt)
REVERT: B  189 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7684 (tt)
REVERT: B  205 GLN cc_start: 0.7878 (mp10) cc_final: 0.7178 (mt0)
REVERT: B  257 MET cc_start: 0.7424 (mmm) cc_final: 0.7206 (mtm)
REVERT: B  482 ASP cc_start: 0.8380 (t0) cc_final: 0.7972 (m-30)
REVERT: B  583 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8396 (t)
REVERT: B  620 ASN cc_start: 0.7977 (p0) cc_final: 0.7666 (t0)
REVERT: C  189 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7778 (tm)
REVERT: C  284 LYS cc_start: 0.8413 (mttm) cc_final: 0.8198 (mtpp)
REVERT: C  329 MET cc_start: 0.8810 (mtp) cc_final: 0.8594 (mtm)
REVERT: C  418 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6722 (pt0)
REVERT: C  470 MET cc_start: 0.8420 (ttm) cc_final: 0.8169 (ttm)
REVERT: C  497 MET cc_start: 0.8213 (tmt) cc_final: 0.7183 (tmt)
REVERT: C  583 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8259 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 175
  average time/residue: 0.9447
  time to fit residues: 186.2771
Evaluate side-chains
  181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  502 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Chi-restraints excluded: chain C residue  588 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 114 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 151 optimal weight:    3.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.145336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.110260 restraints weight = 36716.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.36
r_work: 0.2845 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12672  Z= 0.164
  Angle     :  0.480   4.488  17241  Z= 0.256
  Chirality :  0.036   0.114   1989
  Planarity :  0.004   0.053   2091
  Dihedral  :  8.263 142.157   1854
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.19 %
    Favored  : 81.81 %
  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 aren not related in a simple way.
  whole:  2.71 (0.21), residues: 1593
  helix:  2.35 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.08 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 133 
 TYR   0.006   0.001   TYR A 119 
 PHE   0.013   0.001   PHE B 413 
 TRP   0.006   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12672)
  covalent geometry    : angle       0.47967 (17241)
  hydrogen bonds       : bond        0.05680 (  967)
  hydrogen bonds       : angle       4.14027 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  192 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.7074 (tp) cc_final: 0.6718 (mp)
REVERT: A  307 MET cc_start: 0.8568 (mtm) cc_final: 0.8349 (mtp)
REVERT: A  497 MET cc_start: 0.8289 (tmt) cc_final: 0.7254 (tmt)
REVERT: A  598 MET cc_start: 0.8698 (tpp) cc_final: 0.8227 (tpt)
REVERT: B  189 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7611 (tt)
REVERT: B  205 GLN cc_start: 0.7915 (mp10) cc_final: 0.7139 (mt0)
REVERT: B  257 MET cc_start: 0.7463 (mmm) cc_final: 0.7117 (mtm)
REVERT: B  482 ASP cc_start: 0.8329 (t0) cc_final: 0.7892 (m-30)
REVERT: B  620 ASN cc_start: 0.8167 (p0) cc_final: 0.7749 (t0)
REVERT: C  189 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (tm)
REVERT: C  284 LYS cc_start: 0.8378 (mttm) cc_final: 0.8132 (mtpp)
REVERT: C  329 MET cc_start: 0.8794 (mtp) cc_final: 0.8568 (mtm)
REVERT: C  418 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6652 (pt0)
REVERT: C  470 MET cc_start: 0.8469 (ttm) cc_final: 0.8242 (ttm)
REVERT: C  497 MET cc_start: 0.8182 (tmt) cc_final: 0.7090 (tmt)
REVERT: C  583 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8147 (t)
  outliers start: 25
  outliers final: 13
  residues processed: 181
  average time/residue: 0.9727
  time to fit residues: 198.3093
Evaluate side-chains
  183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  443 THR
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Chi-restraints excluded: chain C residue  588 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 138 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.134858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.097771 restraints weight = 37152.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.48
r_work: 0.2842 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12672  Z= 0.139
  Angle     :  0.458   4.440  17241  Z= 0.244
  Chirality :  0.035   0.111   1989
  Planarity :  0.004   0.052   2091
  Dihedral  :  8.163 140.153   1854
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.11 %
    Favored  : 82.37 %
  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 aren not related in a simple way.
  whole:  2.77 (0.21), residues: 1593
  helix:  2.40 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.06 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 557 
 TYR   0.005   0.001   TYR A 119 
 PHE   0.012   0.001   PHE C 413 
 TRP   0.007   0.001   TRP A 323 
 HIS   0.003   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12672)
  covalent geometry    : angle       0.45763 (17241)
  hydrogen bonds       : bond        0.05223 (  967)
  hydrogen bonds       : angle       4.08106 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6973 (tp) cc_final: 0.6637 (mp)
REVERT: A  307 MET cc_start: 0.8489 (mtm) cc_final: 0.8263 (mtp)
REVERT: A  497 MET cc_start: 0.8285 (tmt) cc_final: 0.7257 (tmt)
REVERT: A  598 MET cc_start: 0.8681 (tpp) cc_final: 0.8209 (tpt)
REVERT: B  189 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7584 (tt)
REVERT: B  205 GLN cc_start: 0.7893 (mp10) cc_final: 0.7077 (mt0)
REVERT: B  257 MET cc_start: 0.7322 (mmm) cc_final: 0.6976 (mtm)
REVERT: B  482 ASP cc_start: 0.8345 (t0) cc_final: 0.7897 (m-30)
REVERT: B  571 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8136 (p0)
REVERT: B  620 ASN cc_start: 0.8169 (p0) cc_final: 0.7725 (t0)
REVERT: C  189 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7644 (tm)
REVERT: C  284 LYS cc_start: 0.8353 (mttm) cc_final: 0.8096 (mtpp)
REVERT: C  329 MET cc_start: 0.8790 (mtp) cc_final: 0.8573 (mtm)
REVERT: C  418 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6596 (pt0)
REVERT: C  470 MET cc_start: 0.8459 (ttm) cc_final: 0.8235 (ttm)
REVERT: C  497 MET cc_start: 0.8180 (tmt) cc_final: 0.7086 (tmt)
REVERT: C  583 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (t)
  outliers start: 19
  outliers final: 13
  residues processed: 176
  average time/residue: 0.9730
  time to fit residues: 193.1942
Evaluate side-chains
  185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  571 ASN
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Chi-restraints excluded: chain C residue  588 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0270
   chunk 110 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9990
   chunk 140 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9644

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.152173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117292 restraints weight = 36184.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.38
r_work: 0.2879 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12672  Z= 0.124
  Angle     :  0.444   4.542  17241  Z= 0.235
  Chirality :  0.034   0.110   1989
  Planarity :  0.004   0.051   2091
  Dihedral  :  8.043 138.148   1854
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.27 %
    Favored  : 82.37 %
  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 aren not related in a simple way.
  whole:  2.89 (0.22), residues: 1593
  helix:  2.48 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -1.02 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 589 
 TYR   0.004   0.001   TYR C 309 
 PHE   0.011   0.001   PHE C 413 
 TRP   0.008   0.001   TRP A 323 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12672)
  covalent geometry    : angle       0.44445 (17241)
  hydrogen bonds       : bond        0.04891 (  967)
  hydrogen bonds       : angle       4.01280 ( 2856)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.6983 (tp) cc_final: 0.6662 (mp)
REVERT: A  307 MET cc_start: 0.8505 (mtm) cc_final: 0.8287 (mtp)
REVERT: A  497 MET cc_start: 0.8287 (tmt) cc_final: 0.7263 (tmt)
REVERT: A  598 MET cc_start: 0.8703 (tpp) cc_final: 0.8234 (tpt)
REVERT: B  189 LEU cc_start: 0.7893 (tm) cc_final: 0.7630 (tt)
REVERT: B  205 GLN cc_start: 0.7909 (mp10) cc_final: 0.7123 (mt0)
REVERT: B  257 MET cc_start: 0.7252 (mmm) cc_final: 0.6954 (mtm)
REVERT: B  482 ASP cc_start: 0.8372 (t0) cc_final: 0.7947 (m-30)
REVERT: B  620 ASN cc_start: 0.8183 (p0) cc_final: 0.7706 (t0)
REVERT: C  189 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7695 (tm)
REVERT: C  284 LYS cc_start: 0.8335 (mttm) cc_final: 0.8094 (mtpp)
REVERT: C  418 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6630 (pt0)
REVERT: C  470 MET cc_start: 0.8459 (ttm) cc_final: 0.8215 (ttm)
REVERT: C  497 MET cc_start: 0.8222 (tmt) cc_final: 0.7119 (tmt)
REVERT: C  583 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8193 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 175
  average time/residue: 0.9835
  time to fit residues: 193.9862
Evaluate side-chains
  184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  418 GLU
Chi-restraints excluded: chain C residue  435 SER
Chi-restraints excluded: chain C residue  443 THR
Chi-restraints excluded: chain C residue  577 ILE
Chi-restraints excluded: chain C residue  583 THR
Chi-restraints excluded: chain C residue  588 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0470
   chunk 14 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.7678

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.156484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.126663 restraints weight = 36196.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.17
r_work: 0.2928 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12672  Z= 0.113
  Angle     :  0.436   4.409  17241  Z= 0.230
  Chirality :  0.034   0.110   1989
  Planarity :  0.004   0.049   2091
  Dihedral  :  7.906 136.252   1854
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.67 %
    Favored  : 82.13 %
  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 aren not related in a simple way.
  whole:  3.00 (0.22), residues: 1593
  helix:  2.56 (0.15), residues: 1317
  sheet:  None (None), residues: 0
  loop : -0.99 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 557 
 TYR   0.004   0.001   TYR B 216 
 PHE   0.009   0.001   PHE C 413 
 TRP   0.009   0.001   TRP A 323 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12672)
  covalent geometry    : angle       0.43611 (17241)
  hydrogen bonds       : bond        0.04578 (  967)
  hydrogen bonds       : angle       3.95855 ( 2856)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6525.25 seconds
wall clock time: 111 minutes 21.97 seconds (6681.97 seconds total)