Starting phenix.real_space_refine
on Wed Mar  4 04:20:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nsg_12566/03_2026/7nsg_12566.map"
  }
  resolution = 3.34
  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=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      69      5.16       5
     C    6855      2.51       5
     N    1575      2.21       5
     O    1848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10356
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3255
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 12, 'TRANS': 417}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 197
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 7, 185
          Unusual residues: {'PC1': 5, 'UR5': 1, 'Y01': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 157
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PC1:plan-2': 2}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 7, 185
          Unusual residues: {'PC1': 5, 'UR8': 1, 'Y01': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 157
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PC1:plan-2': 2}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 171
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AUR5 A 501 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 AUR5 A 501 " occ=0.50
    residue:
      pdb=" N  BUR8 A 502 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 BUR8 A 502 " occ=0.50
    residue:
      pdb=" N  AUR5 B 501 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 AUR5 B 501 " occ=0.50
    residue:
      pdb=" N  BUR8 B 502 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 BUR8 B 502 " occ=0.50
    residue:
      pdb=" N  AUR5 C 501 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 AUR5 C 501 " occ=0.50
    residue:
      pdb=" N  BUR8 C 502 " occ=0.50
      ... (10 atoms not shown)
      pdb=" O3 BUR8 C 502 " occ=0.50
  Time building chain proxies: 2.84, per 1000 atoms: 0.27
  Number of scatterers: 10356
  At special positions: 0
  Unit cell: (116.202, 116.202, 89.052, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      69     16.00
     P       9     15.00
     O    1848      8.00
     N    1575      7.00
     C    6855      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 438.7 milliseconds
  

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2394

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 3 sheets defined
      81.2% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 18
    Processing helix  chain 'A' and resid 18 through 40
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 3.566A  pdb=" N   LYS A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 86
      removed outlier: 3.621A  pdb=" N   ILE A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 117
      removed outlier: 3.513A  pdb=" N   ARG A  93 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 150
      removed outlier: 4.230A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 211 through 228
      removed outlier: 3.504A  pdb=" N   LEU A 215 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 273
      removed outlier: 3.814A  pdb=" N   VAL A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      Proline residue:  A 259  - end of helix
      removed outlier: 3.865A  pdb=" N   GLU A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 298
    Processing helix  chain 'A' and resid 299 through 309
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.765A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 351 through 363
      removed outlier: 4.307A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 367 through 385
      removed outlier: 3.653A  pdb=" N   ALA A 371 " --> pdb=" O   MET A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 403
      removed outlier: 3.627A  pdb=" N   THR A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 4.092A  pdb=" N   ALA A 408 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA A 409 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 413
      No H-bonds generated for 'chain 'A' and resid 411 through 413'
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 3.542A  pdb=" N   LEU A 423 " --> pdb=" O   MET A 419 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 436
      removed outlier: 3.801A  pdb=" N   ASP A 432 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   THR A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 466
      removed outlier: 3.843A  pdb=" N   LEU A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ARG A 445 " --> pdb=" O   TRP A 441 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 476
      removed outlier: 3.616A  pdb=" N   GLU A 471 " --> pdb=" O   LYS A 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 18
    Processing helix  chain 'B' and resid 18 through 40
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.566A  pdb=" N   LYS B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 3.621A  pdb=" N   ILE B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 117
      removed outlier: 3.514A  pdb=" N   ARG B  93 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 150
      removed outlier: 4.230A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE B 150 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 158
    Processing helix  chain 'B' and resid 211 through 228
      removed outlier: 3.505A  pdb=" N   LEU B 215 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 273
      removed outlier: 3.814A  pdb=" N   VAL B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      Proline residue:  B 259  - end of helix
      removed outlier: 3.866A  pdb=" N   GLU B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 298
    Processing helix  chain 'B' and resid 299 through 309
    Processing helix  chain 'B' and resid 312 through 320
      removed outlier: 3.766A  pdb=" N   PHE B 316 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 351 through 363
      removed outlier: 4.306A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      Proline residue:  B 360  - end of helix
    Processing helix  chain 'B' and resid 367 through 385
      removed outlier: 3.654A  pdb=" N   ALA B 371 " --> pdb=" O   MET B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 403
      removed outlier: 3.627A  pdb=" N   THR B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 409
      removed outlier: 4.091A  pdb=" N   ALA B 408 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA B 409 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 413
      No H-bonds generated for 'chain 'B' and resid 411 through 413'
    Processing helix  chain 'B' and resid 414 through 427
      removed outlier: 3.541A  pdb=" N   LEU B 423 " --> pdb=" O   MET B 419 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.801A  pdb=" N   ASP B 432 " --> pdb=" O   PRO B 429 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR B 434 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.844A  pdb=" N   LEU B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ARG B 445 " --> pdb=" O   TRP B 441 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   PHE B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLY B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 3.616A  pdb=" N   GLU B 471 " --> pdb=" O   LYS B 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 18
    Processing helix  chain 'C' and resid 18 through 40
    Processing helix  chain 'C' and resid 53 through 66
      removed outlier: 3.566A  pdb=" N   LYS C  64 " --> pdb=" O   MET C  60 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 86
      removed outlier: 3.621A  pdb=" N   ILE C  72 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 117
      removed outlier: 3.514A  pdb=" N   ARG C  93 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 150
      removed outlier: 4.230A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE C 150 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 158
    Processing helix  chain 'C' and resid 211 through 228
      removed outlier: 3.504A  pdb=" N   LEU C 215 " --> pdb=" O   ASN C 211 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS C 228 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 273
      removed outlier: 3.814A  pdb=" N   VAL C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
      Proline residue:  C 259  - end of helix
      removed outlier: 3.866A  pdb=" N   GLU C 272 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 298
    Processing helix  chain 'C' and resid 299 through 309
    Processing helix  chain 'C' and resid 312 through 320
      removed outlier: 3.766A  pdb=" N   PHE C 316 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET C 320 " --> pdb=" O   PHE C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 330
    Processing helix  chain 'C' and resid 336 through 346
    Processing helix  chain 'C' and resid 351 through 363
      removed outlier: 4.307A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
      Proline residue:  C 360  - end of helix
    Processing helix  chain 'C' and resid 367 through 385
      removed outlier: 3.654A  pdb=" N   ALA C 371 " --> pdb=" O   MET C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 403
      removed outlier: 3.627A  pdb=" N   THR C 402 " --> pdb=" O   SER C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 409
      removed outlier: 4.092A  pdb=" N   ALA C 408 " --> pdb=" O   SER C 405 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA C 409 " --> pdb=" O   ILE C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 413
      No H-bonds generated for 'chain 'C' and resid 411 through 413'
    Processing helix  chain 'C' and resid 414 through 427
      removed outlier: 3.542A  pdb=" N   LEU C 423 " --> pdb=" O   MET C 419 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL C 426 " --> pdb=" O   VAL C 422 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY C 427 " --> pdb=" O   LEU C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 436
      removed outlier: 3.801A  pdb=" N   ASP C 432 " --> pdb=" O   PRO C 429 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   THR C 434 " --> pdb=" O   GLU C 431 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 466
      removed outlier: 3.845A  pdb=" N   LEU C 443 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ARG C 445 " --> pdb=" O   TRP C 441 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   PHE C 446 " --> pdb=" O   LEU C 442 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY C 460 " --> pdb=" O   ALA C 456 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 467 through 476
      removed outlier: 3.615A  pdb=" N   GLU C 471 " --> pdb=" O   LYS C 467 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 168
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 168
    Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 168

    708 hydrogen bonds defined for protein.
    2079 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: 1.79

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1623
        1.32 -     1.44: 2352
        1.44 -     1.56: 6381
        1.56 -     1.68: 18
        1.68 -     1.80: 123
  Bond restraints: 10497
  Sorted by residual:
  bond pdb=" C21 PC1 B 506 "
       pdb=" O22 PC1 B 506 "
    ideal  model  delta    sigma   weight residual
    1.205  1.340 -0.135 2.00e-02 2.50e+03 4.55e+01
  bond pdb=" C21 PC1 A 506 "
       pdb=" O22 PC1 A 506 "
    ideal  model  delta    sigma   weight residual
    1.205  1.340 -0.135 2.00e-02 2.50e+03 4.53e+01
  bond pdb=" C21 PC1 C 506 "
       pdb=" O22 PC1 C 506 "
    ideal  model  delta    sigma   weight residual
    1.205  1.339 -0.134 2.00e-02 2.50e+03 4.52e+01
  bond pdb=" C21 PC1 A 506 "
       pdb=" O21 PC1 A 506 "
    ideal  model  delta    sigma   weight residual
    1.331  1.200  0.131 2.00e-02 2.50e+03 4.32e+01
  bond pdb=" C21 PC1 C 506 "
       pdb=" O21 PC1 C 506 "
    ideal  model  delta    sigma   weight residual
    1.331  1.201  0.130 2.00e-02 2.50e+03 4.25e+01
  ... (remaining 10492 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 13872
        2.83 -     5.66: 247
        5.66 -     8.49: 47
        8.49 -    11.32: 3
       11.32 -    14.15: 6
  Bond angle restraints: 14175
  Sorted by residual:
  angle pdb=" N   ILE A 391 "
        pdb=" CA  ILE A 391 "
        pdb=" C   ILE A 391 "
      ideal   model   delta    sigma   weight residual
     112.90  106.66    6.24 9.60e-01 1.09e+00 4.23e+01
  angle pdb=" N   ILE B 391 "
        pdb=" CA  ILE B 391 "
        pdb=" C   ILE B 391 "
      ideal   model   delta    sigma   weight residual
     112.90  106.67    6.23 9.60e-01 1.09e+00 4.21e+01
  angle pdb=" N   ILE C 391 "
        pdb=" CA  ILE C 391 "
        pdb=" C   ILE C 391 "
      ideal   model   delta    sigma   weight residual
     112.90  106.67    6.23 9.60e-01 1.09e+00 4.20e+01
  angle pdb=" C22 PC1 A 506 "
        pdb=" C21 PC1 A 506 "
        pdb=" O22 PC1 A 506 "
      ideal   model   delta    sigma   weight residual
     125.37  111.22   14.15 3.00e+00 1.11e-01 2.22e+01
  angle pdb=" C22 PC1 B 506 "
        pdb=" C21 PC1 B 506 "
        pdb=" O22 PC1 B 506 "
      ideal   model   delta    sigma   weight residual
     125.37  111.28   14.09 3.00e+00 1.11e-01 2.21e+01
  ... (remaining 14170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 5981
       17.90 -    35.79: 547
       35.79 -    53.69: 93
       53.69 -    71.58: 24
       71.58 -    89.48: 9
  Dihedral angle restraints: 6654
    sinusoidal: 2949
      harmonic: 3705
  Sorted by residual:
  dihedral pdb=" CA  GLU B  48 "
           pdb=" C   GLU B  48 "
           pdb=" N   LYS B  49 "
           pdb=" CA  LYS B  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  GLU C  48 "
           pdb=" C   GLU C  48 "
           pdb=" N   LYS C  49 "
           pdb=" CA  LYS C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  GLU A  48 "
           pdb=" C   GLU A  48 "
           pdb=" N   LYS A  49 "
           pdb=" CA  LYS A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.44   17.56     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1226
       0.048 -    0.095: 406
       0.095 -    0.143: 104
       0.143 -    0.190: 25
       0.190 -    0.238: 6
  Chirality restraints: 1767
  Sorted by residual:
  chirality pdb=" C1 BUR8 C 502 "
            pdb=" C2 BUR8 C 502 "
            pdb=" C4 BUR8 C 502 "
            pdb=" O1 BUR8 C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.93   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1 BUR8 B 502 "
            pdb=" C2 BUR8 B 502 "
            pdb=" C4 BUR8 B 502 "
            pdb=" O1 BUR8 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.93   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1 BUR8 A 502 "
            pdb=" C2 BUR8 A 502 "
            pdb=" C4 BUR8 A 502 "
            pdb=" O1 BUR8 A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.93   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1764 not shown)

  Planarity restraints: 1677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 301 "   -0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO C 302 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 302 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 302 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 301 "   -0.037 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO B 302 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 302 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 302 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 301 "   -0.037 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A 302 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 302 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 302 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1674 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2968
        2.83 -     3.34: 9327
        3.34 -     3.86: 15903
        3.86 -     4.38: 18601
        4.38 -     4.90: 33103
  Nonbonded interactions: 79902
  Sorted by model distance:
  nonbonded pdb=" O   SER A 331 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   SER B 331 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   SER C 331 "
            pdb=" OG  SER C 331 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OD1 ASP A 444 "
            pdb=" N1 AUR5 A 501 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" OD1 ASP B 444 "
            pdb=" N1 AUR5 B 501 "
     model   vdw
     2.411 3.120
  ... (remaining 79897 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: 0.02
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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.960
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.009   0.135  10497  Z= 0.406
  Angle     :  1.005  14.147  14175  Z= 0.521
  Chirality :  0.052   0.238   1767
  Planarity :  0.007   0.055   1677
  Dihedral  : 14.071  89.476   4260
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.82 (0.18), residues: 1272
  helix: -2.30 (0.12), residues: 963
  sheet: -1.29 (0.76), residues: 60
  loop : -2.71 (0.33), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 353 
 TYR   0.021   0.003   TYR C 373 
 PHE   0.035   0.003   PHE A 341 
 TRP   0.008   0.001   TRP A 276 
 HIS   0.001   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00927 (10497)
  covalent geometry    : angle       1.00540 (14175)
  hydrogen bonds       : bond        0.15694 (  708)
  hydrogen bonds       : angle       6.06687 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7673 (ptmm)
REVERT: A  258 MET cc_start: 0.7869 (ttp) cc_final: 0.7593 (ttp)
REVERT: A  325 LEU cc_start: 0.8155 (tp) cc_final: 0.7886 (tp)
REVERT: A  353 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7518 (ttm110)
REVERT: A  449 MET cc_start: 0.7640 (ttp) cc_final: 0.7254 (ttt)
REVERT: A  473 MET cc_start: 0.7087 (mtm) cc_final: 0.6473 (tmm)
REVERT: B   39 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7097 (ttt180)
REVERT: B  165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7613 (ptmm)
REVERT: B  258 MET cc_start: 0.7822 (ttp) cc_final: 0.7547 (ttt)
REVERT: B  353 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7532 (ttm110)
REVERT: B  419 MET cc_start: 0.8770 (tpt) cc_final: 0.8229 (tpt)
REVERT: B  449 MET cc_start: 0.7654 (ttp) cc_final: 0.7317 (ttt)
REVERT: C  165 LYS cc_start: 0.8170 (pttt) cc_final: 0.7572 (ptmm)
REVERT: C  248 MET cc_start: 0.8461 (mmm) cc_final: 0.8240 (mmm)
REVERT: C  258 MET cc_start: 0.7831 (ttp) cc_final: 0.7486 (ttp)
REVERT: C  315 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6752 (mmm160)
REVERT: C  353 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7258 (ttm110)
REVERT: C  419 MET cc_start: 0.8660 (tpt) cc_final: 0.8020 (tpt)
REVERT: C  449 MET cc_start: 0.7530 (ttp) cc_final: 0.7198 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1170
  time to fit residues: 25.2895
Evaluate side-chains
  134 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 413 GLN
B 413 GLN
C 413 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.147290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.098339 restraints weight = 11387.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 1.86
r_work: 0.2720 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10497  Z= 0.129
  Angle     :  0.529   8.583  14175  Z= 0.277
  Chirality :  0.038   0.139   1767
  Planarity :  0.004   0.037   1677
  Dihedral  : 10.225  80.986   2064
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.03 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.23), residues: 1272
  helix: -0.00 (0.17), residues: 966
  sheet: -1.12 (0.76), residues: 60
  loop : -2.56 (0.32), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 356 
 TYR   0.011   0.001   TYR C 257 
 PHE   0.017   0.002   PHE A 341 
 TRP   0.005   0.001   TRP C  19 
 HIS   0.000   0.000   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10497)
  covalent geometry    : angle       0.52915 (14175)
  hydrogen bonds       : bond        0.05011 (  708)
  hydrogen bonds       : angle       4.10067 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8820 (mmt) cc_final: 0.8580 (mmm)
REVERT: A  165 LYS cc_start: 0.8130 (pttt) cc_final: 0.7538 (ptmm)
REVERT: A  258 MET cc_start: 0.8092 (ttp) cc_final: 0.7726 (ttt)
REVERT: A  353 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7450 (ttm110)
REVERT: A  356 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7554 (mmt-90)
REVERT: A  449 MET cc_start: 0.7862 (ttp) cc_final: 0.7556 (ttt)
REVERT: B  160 GLN cc_start: 0.8989 (pt0) cc_final: 0.8570 (pt0)
REVERT: B  165 LYS cc_start: 0.8085 (pttt) cc_final: 0.7423 (ptmm)
REVERT: B  258 MET cc_start: 0.8057 (ttp) cc_final: 0.7793 (ttt)
REVERT: B  353 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7515 (ttm110)
REVERT: B  449 MET cc_start: 0.7818 (ttp) cc_final: 0.7576 (ttp)
REVERT: C  165 LYS cc_start: 0.8127 (pttt) cc_final: 0.7500 (ptmm)
REVERT: C  258 MET cc_start: 0.8204 (ttp) cc_final: 0.7860 (ttt)
REVERT: C  315 ARG cc_start: 0.7403 (mmt90) cc_final: 0.6706 (mmm160)
REVERT: C  353 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7244 (ttm110)
REVERT: C  356 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7557 (mmt-90)
  outliers start: 10
  outliers final: 8
  residues processed: 154
  average time/residue: 0.1206
  time to fit residues: 24.7598
Evaluate side-chains
  150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 104 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.145128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.095669 restraints weight = 11503.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 1.87
r_work: 0.2680 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2518 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2495 r_free = 0.2495    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2494 r_free = 0.2494    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10497  Z= 0.174
  Angle     :  0.554   7.995  14175  Z= 0.286
  Chirality :  0.040   0.157   1767
  Planarity :  0.004   0.034   1677
  Dihedral  :  9.986  81.164   2064
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.14 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.24), residues: 1272
  helix:  0.66 (0.17), residues: 969
  sheet: -1.09 (0.74), residues: 60
  loop : -2.32 (0.34), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 356 
 TYR   0.010   0.001   TYR A 373 
 PHE   0.015   0.002   PHE A 159 
 TRP   0.005   0.001   TRP C  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (10497)
  covalent geometry    : angle       0.55381 (14175)
  hydrogen bonds       : bond        0.05222 (  708)
  hydrogen bonds       : angle       3.99912 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8225 (pttt) cc_final: 0.7628 (ptmm)
REVERT: A  258 MET cc_start: 0.8164 (ttp) cc_final: 0.7802 (ttt)
REVERT: A  353 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7456 (ttm110)
REVERT: A  356 ARG cc_start: 0.8009 (mmt-90) cc_final: 0.7753 (mmt-90)
REVERT: A  449 MET cc_start: 0.8134 (ttp) cc_final: 0.7822 (ttt)
REVERT: B  165 LYS cc_start: 0.8151 (pttt) cc_final: 0.7510 (ptmm)
REVERT: B  206 TYR cc_start: 0.9190 (m-80) cc_final: 0.8849 (m-80)
REVERT: B  258 MET cc_start: 0.8183 (ttp) cc_final: 0.7977 (ttt)
REVERT: B  353 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7397 (ttm110)
REVERT: B  449 MET cc_start: 0.8098 (ttp) cc_final: 0.7827 (ttp)
REVERT: C   39 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7306 (mtp180)
REVERT: C  165 LYS cc_start: 0.8231 (pttt) cc_final: 0.7608 (ptmm)
REVERT: C  258 MET cc_start: 0.8299 (ttp) cc_final: 0.7961 (ttt)
REVERT: C  315 ARG cc_start: 0.7564 (mmt90) cc_final: 0.6993 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.7280 (ttm110)
REVERT: C  356 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7648 (mtt-85)
REVERT: C  449 MET cc_start: 0.7932 (ttp) cc_final: 0.7585 (ttp)
REVERT: C  473 MET cc_start: 0.6646 (mtm) cc_final: 0.6368 (mtm)
  outliers start: 14
  outliers final: 6
  residues processed: 156
  average time/residue: 0.1249
  time to fit residues: 25.7953
Evaluate side-chains
  149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 143
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0050
   chunk 17 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.148919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.099856 restraints weight = 11537.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.88
r_work: 0.2749 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10497  Z= 0.105
  Angle     :  0.478   8.027  14175  Z= 0.247
  Chirality :  0.037   0.123   1767
  Planarity :  0.003   0.031   1677
  Dihedral  :  9.371  77.662   2064
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.90 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1272
  helix:  1.25 (0.18), residues: 954
  sheet: -0.87 (0.74), residues: 60
  loop : -1.76 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 356 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.009   0.001   PHE A 159 
 TRP   0.005   0.001   TRP B 441 
 HIS   0.001   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (10497)
  covalent geometry    : angle       0.47810 (14175)
  hydrogen bonds       : bond        0.04122 (  708)
  hydrogen bonds       : angle       3.75703 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8123 (pttt) cc_final: 0.7483 (ptmm)
REVERT: A  255 MET cc_start: 0.8827 (mmm) cc_final: 0.8611 (mmm)
REVERT: A  258 MET cc_start: 0.8209 (ttp) cc_final: 0.7830 (ttt)
REVERT: A  353 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7619 (ttm110)
REVERT: A  449 MET cc_start: 0.8075 (ttp) cc_final: 0.7751 (ttt)
REVERT: B   39 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7156 (mtp180)
REVERT: B  160 GLN cc_start: 0.8990 (pt0) cc_final: 0.8759 (pt0)
REVERT: B  165 LYS cc_start: 0.8115 (pttt) cc_final: 0.7509 (ptmm)
REVERT: B  258 MET cc_start: 0.8111 (ttp) cc_final: 0.7901 (ttt)
REVERT: B  449 MET cc_start: 0.8016 (ttp) cc_final: 0.7799 (ttp)
REVERT: C   39 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7254 (mtp180)
REVERT: C  165 LYS cc_start: 0.8197 (pttt) cc_final: 0.7587 (ptmm)
REVERT: C  258 MET cc_start: 0.8205 (ttp) cc_final: 0.7871 (ttt)
REVERT: C  315 ARG cc_start: 0.7610 (mmt90) cc_final: 0.7003 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7242 (ttm110)
REVERT: C  449 MET cc_start: 0.8010 (ttp) cc_final: 0.7636 (ttp)
REVERT: C  473 MET cc_start: 0.6450 (mtm) cc_final: 0.6231 (mtm)
  outliers start: 17
  outliers final: 9
  residues processed: 167
  average time/residue: 0.1164
  time to fit residues: 26.1182
Evaluate side-chains
  152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  342 ARG
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  354 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 28 optimal weight:    0.0770
   chunk 69 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 122 optimal weight:    8.9990
   chunk 117 optimal weight:    0.2980
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.0342

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.148008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.099016 restraints weight = 11357.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.85
r_work: 0.2736 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10497  Z= 0.117
  Angle     :  0.495   9.480  14175  Z= 0.251
  Chirality :  0.038   0.129   1767
  Planarity :  0.003   0.029   1677
  Dihedral  :  9.157  74.074   2064
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.56 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.25), residues: 1272
  helix:  1.42 (0.18), residues: 957
  sheet: -0.77 (0.75), residues: 60
  loop : -1.40 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 356 
 TYR   0.008   0.001   TYR A 162 
 PHE   0.011   0.001   PHE C 159 
 TRP   0.005   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10497)
  covalent geometry    : angle       0.49483 (14175)
  hydrogen bonds       : bond        0.04237 (  708)
  hydrogen bonds       : angle       3.71738 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8132 (pttt) cc_final: 0.7486 (ptmm)
REVERT: A  255 MET cc_start: 0.8769 (mmm) cc_final: 0.8453 (mmm)
REVERT: A  258 MET cc_start: 0.8193 (ttp) cc_final: 0.7822 (ttt)
REVERT: A  353 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7592 (ttm110)
REVERT: A  449 MET cc_start: 0.8089 (ttp) cc_final: 0.7761 (ttt)
REVERT: A  473 MET cc_start: 0.6461 (mtm) cc_final: 0.6214 (tmm)
REVERT: B   39 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7284 (mtp180)
REVERT: B  160 GLN cc_start: 0.8934 (pt0) cc_final: 0.8677 (pt0)
REVERT: B  165 LYS cc_start: 0.8126 (pttt) cc_final: 0.7500 (ptmm)
REVERT: C   39 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7369 (mtp180)
REVERT: C  165 LYS cc_start: 0.8211 (pttt) cc_final: 0.7598 (ptmm)
REVERT: C  258 MET cc_start: 0.8155 (ttp) cc_final: 0.7832 (ttt)
REVERT: C  315 ARG cc_start: 0.7571 (mmt90) cc_final: 0.6989 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7224 (ttm110)
REVERT: C  449 MET cc_start: 0.7869 (ttp) cc_final: 0.7586 (ttt)
  outliers start: 23
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1177
  time to fit residues: 24.8795
Evaluate side-chains
  155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  342 ARG
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0770
   chunk 103 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0870
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.149524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.100942 restraints weight = 11422.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.82
r_work: 0.2765 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2577 r_free = 0.2577    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2577 r_free = 0.2577    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10497  Z= 0.101
  Angle     :  0.471   8.607  14175  Z= 0.239
  Chirality :  0.037   0.122   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  8.850  70.154   2064
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.88 %
    Favored  : 84.89 %
  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 are not related in a simple way.
  whole:  1.48 (0.25), residues: 1272
  helix:  1.71 (0.18), residues: 954
  sheet: -0.74 (0.75), residues: 60
  loop : -1.33 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 353 
 TYR   0.008   0.001   TYR A 162 
 PHE   0.008   0.001   PHE A 159 
 TRP   0.006   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (10497)
  covalent geometry    : angle       0.47056 (14175)
  hydrogen bonds       : bond        0.03850 (  708)
  hydrogen bonds       : angle       3.62174 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8923 (mmt) cc_final: 0.8634 (mmm)
REVERT: A  165 LYS cc_start: 0.8115 (pttt) cc_final: 0.7525 (ptmm)
REVERT: A  255 MET cc_start: 0.8733 (mmm) cc_final: 0.8405 (mmm)
REVERT: A  258 MET cc_start: 0.8207 (ttp) cc_final: 0.7808 (ttt)
REVERT: A  353 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7421 (ttm110)
REVERT: A  449 MET cc_start: 0.8145 (ttp) cc_final: 0.7808 (ttt)
REVERT: B   39 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7194 (mtp180)
REVERT: B  165 LYS cc_start: 0.8132 (pttt) cc_final: 0.7512 (ptmm)
REVERT: C   39 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7442 (mtp180)
REVERT: C  165 LYS cc_start: 0.8221 (pttt) cc_final: 0.7622 (ptmm)
REVERT: C  258 MET cc_start: 0.8162 (ttp) cc_final: 0.7842 (ttt)
REVERT: C  315 ARG cc_start: 0.7513 (mmt90) cc_final: 0.6953 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7311 (ttm110)
  outliers start: 13
  outliers final: 11
  residues processed: 147
  average time/residue: 0.1118
  time to fit residues: 22.2755
Evaluate side-chains
  151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 117 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.145398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.096108 restraints weight = 11283.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.84
r_work: 0.2686 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2521 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2495 r_free = 0.2495    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2495 r_free = 0.2495    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10497  Z= 0.166
  Angle     :  0.536   8.193  14175  Z= 0.274
  Chirality :  0.040   0.151   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  9.339  70.466   2064
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.07 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.25), residues: 1272
  helix:  1.56 (0.17), residues: 957
  sheet: -0.78 (0.76), residues: 60
  loop : -1.21 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.008   0.001   TYR B 162 
 PHE   0.015   0.002   PHE C 240 
 TRP   0.004   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10497)
  covalent geometry    : angle       0.53558 (14175)
  hydrogen bonds       : bond        0.04856 (  708)
  hydrogen bonds       : angle       3.79591 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8189 (pttt) cc_final: 0.7587 (ptmm)
REVERT: A  258 MET cc_start: 0.8218 (ttp) cc_final: 0.7845 (ttt)
REVERT: A  353 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7420 (ttm110)
REVERT: A  449 MET cc_start: 0.8088 (ttp) cc_final: 0.7726 (ttt)
REVERT: B   39 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7301 (mtp180)
REVERT: B  165 LYS cc_start: 0.8112 (pttt) cc_final: 0.7482 (ptmm)
REVERT: C   39 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7416 (mtp180)
REVERT: C  165 LYS cc_start: 0.8229 (pttt) cc_final: 0.7621 (ptmm)
REVERT: C  258 MET cc_start: 0.8177 (ttp) cc_final: 0.7843 (ttt)
REVERT: C  315 ARG cc_start: 0.7536 (mmt90) cc_final: 0.6970 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7378 (ttm110)
  outliers start: 19
  outliers final: 14
  residues processed: 151
  average time/residue: 0.1051
  time to fit residues: 21.7382
Evaluate side-chains
  150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  342 ARG
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 59 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 127 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.148222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.099531 restraints weight = 11234.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.82
r_work: 0.2742 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2577 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10497  Z= 0.109
  Angle     :  0.484   8.346  14175  Z= 0.248
  Chirality :  0.037   0.127   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  9.022  68.852   2064
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.45 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.25), residues: 1272
  helix:  1.81 (0.18), residues: 957
  sheet: -0.77 (0.75), residues: 60
  loop : -1.10 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 356 
 TYR   0.011   0.001   TYR C 206 
 PHE   0.009   0.001   PHE A 159 
 TRP   0.006   0.001   TRP A 441 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10497)
  covalent geometry    : angle       0.48399 (14175)
  hydrogen bonds       : bond        0.04042 (  708)
  hydrogen bonds       : angle       3.69639 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8949 (mmt) cc_final: 0.8629 (mmm)
REVERT: A  165 LYS cc_start: 0.8136 (pttt) cc_final: 0.7542 (ptmm)
REVERT: A  258 MET cc_start: 0.8195 (ttp) cc_final: 0.7812 (ttt)
REVERT: A  353 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7400 (ttm110)
REVERT: A  449 MET cc_start: 0.8128 (ttp) cc_final: 0.7783 (ttt)
REVERT: B   39 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7302 (mtp180)
REVERT: B  165 LYS cc_start: 0.8157 (pttt) cc_final: 0.7541 (ptmm)
REVERT: C   39 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7430 (mtp180)
REVERT: C  165 LYS cc_start: 0.8215 (pttt) cc_final: 0.7605 (ptmm)
REVERT: C  258 MET cc_start: 0.8148 (ttp) cc_final: 0.7828 (ttt)
REVERT: C  315 ARG cc_start: 0.7533 (mmt90) cc_final: 0.6964 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7420 (ttm110)
  outliers start: 14
  outliers final: 11
  residues processed: 149
  average time/residue: 0.1041
  time to fit residues: 21.5436
Evaluate side-chains
  147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:   20.0000
   chunk 118 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.146903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.098040 restraints weight = 11232.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.81
r_work: 0.2714 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2526 r_free = 0.2526    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2526 r_free = 0.2526    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10497  Z= 0.129
  Angle     :  0.506   8.126  14175  Z= 0.260
  Chirality :  0.038   0.135   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  9.095  67.176   2064
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.45 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.25), residues: 1272
  helix:  1.94 (0.18), residues: 942
  sheet: -0.79 (0.75), residues: 60
  loop : -0.87 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.010   0.001   TYR C 206 
 PHE   0.011   0.001   PHE C 240 
 TRP   0.005   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10497)
  covalent geometry    : angle       0.50634 (14175)
  hydrogen bonds       : bond        0.04378 (  708)
  hydrogen bonds       : angle       3.74888 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8187 (pttt) cc_final: 0.7586 (ptmm)
REVERT: A  258 MET cc_start: 0.8212 (ttp) cc_final: 0.7842 (ttt)
REVERT: A  353 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7423 (ttm110)
REVERT: A  449 MET cc_start: 0.8154 (ttp) cc_final: 0.7802 (ttt)
REVERT: B   39 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7282 (mtp180)
REVERT: B  165 LYS cc_start: 0.8171 (pttt) cc_final: 0.7555 (ptmm)
REVERT: C   39 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7439 (mtp180)
REVERT: C  165 LYS cc_start: 0.8221 (pttt) cc_final: 0.7619 (ptmm)
REVERT: C  258 MET cc_start: 0.8190 (ttp) cc_final: 0.7870 (ttt)
REVERT: C  315 ARG cc_start: 0.7541 (mmt90) cc_final: 0.6973 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7461 (ttm110)
  outliers start: 13
  outliers final: 13
  residues processed: 144
  average time/residue: 0.1001
  time to fit residues: 20.0138
Evaluate side-chains
  148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.148441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.099316 restraints weight = 11403.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.86
r_work: 0.2738 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2572 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2545 r_free = 0.2545    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2545 r_free = 0.2545    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10497  Z= 0.114
  Angle     :  0.491   8.270  14175  Z= 0.252
  Chirality :  0.038   0.133   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  8.980  65.765   2064
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.64 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.25), residues: 1272
  helix:  1.88 (0.18), residues: 960
  sheet: -0.79 (0.75), residues: 60
  loop : -1.02 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 356 
 TYR   0.010   0.001   TYR C 206 
 PHE   0.009   0.001   PHE C 159 
 TRP   0.005   0.001   TRP A  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10497)
  covalent geometry    : angle       0.49112 (14175)
  hydrogen bonds       : bond        0.04103 (  708)
  hydrogen bonds       : angle       3.73688 ( 2079)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8957 (mmt) cc_final: 0.8632 (mmm)
REVERT: A  165 LYS cc_start: 0.8128 (pttt) cc_final: 0.7539 (ptmm)
REVERT: A  258 MET cc_start: 0.8195 (ttp) cc_final: 0.7806 (ttt)
REVERT: A  353 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7441 (ttm110)
REVERT: A  449 MET cc_start: 0.8136 (ttp) cc_final: 0.7796 (ttt)
REVERT: B   39 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7281 (mtp180)
REVERT: B  165 LYS cc_start: 0.8187 (pttt) cc_final: 0.7542 (ptmm)
REVERT: C   39 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7442 (mtp180)
REVERT: C  165 LYS cc_start: 0.8203 (pttt) cc_final: 0.7598 (ptmm)
REVERT: C  258 MET cc_start: 0.8163 (ttp) cc_final: 0.7840 (ttt)
REVERT: C  315 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7039 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7187 (ttp-110)
  outliers start: 12
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1071
  time to fit residues: 20.9374
Evaluate side-chains
  144 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  354 ILE
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 79 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 44 optimal weight:    0.1980
   chunk 14 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.149707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.100995 restraints weight = 11522.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.85
r_work: 0.2763 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058  10497  Z= 0.103
  Angle     :  0.479   8.414  14175  Z= 0.245
  Chirality :  0.037   0.152   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  8.700  64.343   2064
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.92 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.25), residues: 1272
  helix:  2.10 (0.18), residues: 942
  sheet: -0.84 (0.74), residues: 60
  loop : -0.78 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.010   0.001   TYR C 206 
 PHE   0.009   0.001   PHE A 159 
 TRP   0.006   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10497)
  covalent geometry    : angle       0.47931 (14175)
  hydrogen bonds       : bond        0.03810 (  708)
  hydrogen bonds       : angle       3.68616 ( 2079)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2670.20 seconds
wall clock time: 46 minutes 13.25 seconds (2773.25 seconds total)