Starting phenix.real_space_refine
on Mon Jul 28 23:28:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_12566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_12566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_12566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_12566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2025/7nsg_12566.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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:
    C, B
  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: 6.98, per 1000 atoms: 0.67
  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: 2.74
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.01
  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: 2.87

  Time building geometry restraints manager: 3.19 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.600
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.650
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.130
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A 276 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.035   0.003   PHE A 341 
 TYR   0.021   0.003   TYR C 373 
 ARG   0.003   0.000   ARG B 353 

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

*********************** 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  : 1.029 
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: 0.7847 (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: 0.7086 (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: 0.8169 (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: 0.8659 (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: 0.2746
  time to fit residues: 59.4049
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  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.147693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.098753 restraints weight = 11372.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.86
r_work: 0.2723 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2535 r_free = 0.2535    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10497  Z= 0.127
  Angle     :  0.528   8.543  14175  Z= 0.277
  Chirality :  0.038   0.138   1767
  Planarity :  0.004   0.037   1677
  Dihedral  : 10.229  80.980   2064
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.74 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.23), residues: 1272
  helix: -0.02 (0.17), residues: 966
  sheet: -1.11 (0.76), residues: 60
  loop : -2.57 (0.32), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  19 
 HIS   0.000   0.000   HIS A 296 
 PHE   0.017   0.002   PHE A 341 
 TYR   0.011   0.001   TYR A 373 
 ARG   0.002   0.000   ARG B 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05054 (  708)
  hydrogen bonds       : angle       4.12204 ( 2079)
  covalent geometry    : bond        0.00276 (10497)
  covalent geometry    : angle       0.52829 (14175)

*********************** 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
  162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8976 (mmt) cc_final: 0.8693 (mmm)
REVERT: A  165 LYS cc_start: 0.8183 (pttt) cc_final: 0.7589 (ptmm)
REVERT: A  258 MET cc_start: 0.8264 (ttp) cc_final: 0.7897 (ttt)
REVERT: A  353 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7387 (ttm110)
REVERT: A  356 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7591 (mmt-90)
REVERT: A  449 MET cc_start: 0.8096 (ttp) cc_final: 0.7801 (ttt)
REVERT: B  160 GLN cc_start: 0.9058 (pt0) cc_final: 0.8641 (pt0)
REVERT: B  165 LYS cc_start: 0.8111 (pttt) cc_final: 0.7447 (ptmm)
REVERT: B  258 MET cc_start: 0.8193 (ttp) cc_final: 0.7945 (ttt)
REVERT: B  353 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7465 (ttm110)
REVERT: B  449 MET cc_start: 0.8037 (ttp) cc_final: 0.7817 (ttp)
REVERT: C  165 LYS cc_start: 0.8184 (pttt) cc_final: 0.7557 (ptmm)
REVERT: C  258 MET cc_start: 0.8372 (ttp) cc_final: 0.8032 (ttt)
REVERT: C  315 ARG cc_start: 0.7441 (mmt90) cc_final: 0.6703 (mmm160)
REVERT: C  353 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.7188 (ttm110)
  outliers start: 10
  outliers final: 8
  residues processed: 154
  average time/residue: 0.2781
  time to fit residues: 57.9714
Evaluate side-chains
  152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
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 14 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 126 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.149175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.100139 restraints weight = 11434.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.87
r_work: 0.2749 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2561 r_free = 0.2561    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2561 r_free = 0.2561    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10497  Z= 0.112
  Angle     :  0.488   8.045  14175  Z= 0.251
  Chirality :  0.037   0.125   1767
  Planarity :  0.003   0.031   1677
  Dihedral  :  9.261  76.383   2064
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.95 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1272
  helix:  1.05 (0.18), residues: 936
  sheet: -0.90 (0.74), residues: 60
  loop : -2.19 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  19 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.010   0.001   PHE B 341 
 TYR   0.010   0.001   TYR A 373 
 ARG   0.003   0.000   ARG C 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  708)
  hydrogen bonds       : angle       3.78427 ( 2079)
  covalent geometry    : bond        0.00246 (10497)
  covalent geometry    : angle       0.48782 (14175)

*********************** 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
  166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 1.128 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8961 (mmt) cc_final: 0.8652 (mmm)
REVERT: A  165 LYS cc_start: 0.8173 (pttt) cc_final: 0.7610 (ptmm)
REVERT: A  255 MET cc_start: 0.8849 (mmm) cc_final: 0.8608 (mmm)
REVERT: A  258 MET cc_start: 0.8213 (ttp) cc_final: 0.7831 (ttt)
REVERT: A  353 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7471 (ttm110)
REVERT: A  356 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7758 (mmt-90)
REVERT: A  449 MET cc_start: 0.8070 (ttp) cc_final: 0.7761 (ttt)
REVERT: B   39 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7179 (mtp180)
REVERT: B  160 GLN cc_start: 0.8982 (pt0) cc_final: 0.8635 (pt0)
REVERT: B  165 LYS cc_start: 0.8115 (pttt) cc_final: 0.7516 (ptmm)
REVERT: B  258 MET cc_start: 0.8083 (ttp) cc_final: 0.7866 (ttt)
REVERT: B  353 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7401 (ttm110)
REVERT: B  449 MET cc_start: 0.8010 (ttp) cc_final: 0.7732 (ttp)
REVERT: C  165 LYS cc_start: 0.8179 (pttt) cc_final: 0.7573 (ptmm)
REVERT: C  258 MET cc_start: 0.8291 (ttp) cc_final: 0.7960 (ttt)
REVERT: C  353 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7188 (ttm110)
REVERT: C  356 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7588 (mtt-85)
REVERT: C  449 MET cc_start: 0.8000 (ttp) cc_final: 0.7644 (ttp)
REVERT: C  473 MET cc_start: 0.6585 (mtm) cc_final: 0.6313 (mtm)
  outliers start: 12
  outliers final: 6
  residues processed: 161
  average time/residue: 0.2955
  time to fit residues: 64.1539
Evaluate side-chains
  154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
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 63 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 119 optimal weight:    0.9990
   chunk 116 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 71 optimal weight:    0.3980
   chunk 120 optimal weight:    0.9980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.148601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.098807 restraints weight = 11246.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.89
r_work: 0.2730 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2563 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10497  Z= 0.129
  Angle     :  0.499   7.868  14175  Z= 0.256
  Chirality :  0.038   0.133   1767
  Planarity :  0.003   0.030   1677
  Dihedral  :  9.200  74.155   2064
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.43 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1272
  helix:  1.31 (0.18), residues: 954
  sheet: -0.87 (0.73), residues: 60
  loop : -1.75 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  19 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.008   0.001   TYR B 373 
 ARG   0.002   0.000   ARG C 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  708)
  hydrogen bonds       : angle       3.75440 ( 2079)
  covalent geometry    : bond        0.00303 (10497)
  covalent geometry    : angle       0.49875 (14175)

*********************** 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
  168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8116 (pttt) cc_final: 0.7520 (ptmm)
REVERT: A  258 MET cc_start: 0.8122 (ttp) cc_final: 0.7751 (ttt)
REVERT: A  353 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7596 (ttm110)
REVERT: A  449 MET cc_start: 0.8031 (ttp) cc_final: 0.7702 (ttt)
REVERT: B   39 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7309 (mtp180)
REVERT: B  160 GLN cc_start: 0.8996 (pt0) cc_final: 0.8636 (pt0)
REVERT: B  165 LYS cc_start: 0.8079 (pttt) cc_final: 0.7446 (ptmm)
REVERT: B  258 MET cc_start: 0.8107 (ttp) cc_final: 0.7891 (ttt)
REVERT: B  449 MET cc_start: 0.8088 (ttp) cc_final: 0.7779 (ttp)
REVERT: C   39 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7330 (mtp180)
REVERT: C  165 LYS cc_start: 0.8126 (pttt) cc_final: 0.7523 (ptmm)
REVERT: C  258 MET cc_start: 0.8209 (ttp) cc_final: 0.7861 (ttt)
REVERT: C  315 ARG cc_start: 0.7695 (mpt-90) cc_final: 0.7154 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7263 (ttm110)
REVERT: C  449 MET cc_start: 0.7891 (ttp) cc_final: 0.7502 (ttp)
REVERT: C  473 MET cc_start: 0.6460 (mtm) cc_final: 0.6235 (mtm)
  outliers start: 20
  outliers final: 13
  residues processed: 161
  average time/residue: 0.4114
  time to fit residues: 91.5327
Evaluate side-chains
  156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 2.701 
-------------------------------------------------------------------------------
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  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  354 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   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 = 0.3583 r_free = 0.3583 target = 0.150704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.101098 restraints weight = 11037.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.88
r_work: 0.2763 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2596 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2596
-------------------------------------------------------------------------------
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: 0.8032
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10497  Z= 0.106
  Angle     :  0.474   7.862  14175  Z= 0.243
  Chirality :  0.037   0.123   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  8.939  71.260   2064
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.90 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.25), residues: 1272
  helix:  1.66 (0.18), residues: 939
  sheet: -0.83 (0.73), residues: 60
  loop : -1.14 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  19 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.008   0.001   PHE A 159 
 TYR   0.024   0.001   TYR A 206 
 ARG   0.003   0.000   ARG C 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  708)
  hydrogen bonds       : angle       3.67074 ( 2079)
  covalent geometry    : bond        0.00229 (10497)
  covalent geometry    : angle       0.47439 (14175)

*********************** 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
  168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8899 (mmt) cc_final: 0.8598 (mmm)
REVERT: A  165 LYS cc_start: 0.8053 (pttt) cc_final: 0.7400 (ptmm)
REVERT: A  255 MET cc_start: 0.8717 (mmm) cc_final: 0.8505 (mmm)
REVERT: A  258 MET cc_start: 0.8098 (ttp) cc_final: 0.7727 (ttt)
REVERT: A  353 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7590 (ttm110)
REVERT: A  449 MET cc_start: 0.8035 (ttp) cc_final: 0.7712 (ttt)
REVERT: A  473 MET cc_start: 0.6615 (mtm) cc_final: 0.6229 (tmm)
REVERT: B   39 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7226 (mtp180)
REVERT: B  160 GLN cc_start: 0.9005 (pt0) cc_final: 0.8758 (pt0)
REVERT: B  165 LYS cc_start: 0.8036 (pttt) cc_final: 0.7409 (ptmm)
REVERT: B  258 MET cc_start: 0.8083 (ttp) cc_final: 0.7823 (ttt)
REVERT: B  449 MET cc_start: 0.7947 (ttp) cc_final: 0.7718 (ttp)
REVERT: C   39 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7355 (mtp180)
REVERT: C  165 LYS cc_start: 0.8123 (pttt) cc_final: 0.7518 (ptmm)
REVERT: C  258 MET cc_start: 0.8149 (ttp) cc_final: 0.7829 (ttt)
REVERT: C  315 ARG cc_start: 0.7671 (mpt-90) cc_final: 0.7104 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7235 (ttm110)
REVERT: C  449 MET cc_start: 0.7836 (ttp) cc_final: 0.7554 (ttt)
  outliers start: 21
  outliers final: 15
  residues processed: 160
  average time/residue: 0.3099
  time to fit residues: 66.6231
Evaluate side-chains
  157 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 107 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0060
   chunk 69 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 89 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3602

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.148470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.098423 restraints weight = 11383.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.90
r_work: 0.2725 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2558 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    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 = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10497  Z= 0.132
  Angle     :  0.506   9.311  14175  Z= 0.257
  Chirality :  0.038   0.135   1767
  Planarity :  0.003   0.028   1677
  Dihedral  :  9.042  70.355   2064
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.84 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.25), residues: 1272
  helix:  1.72 (0.18), residues: 942
  sheet: -0.80 (0.74), residues: 60
  loop : -1.05 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.012   0.001   PHE A 159 
 TYR   0.013   0.001   TYR A 206 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  708)
  hydrogen bonds       : angle       3.72210 ( 2079)
  covalent geometry    : bond        0.00316 (10497)
  covalent geometry    : angle       0.50607 (14175)

*********************** 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
  159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  165 LYS cc_start: 0.8069 (pttt) cc_final: 0.7447 (ptmm)
REVERT: A  255 MET cc_start: 0.8774 (mmm) cc_final: 0.8427 (mmm)
REVERT: A  258 MET cc_start: 0.8123 (ttp) cc_final: 0.7759 (ttt)
REVERT: A  353 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7439 (ttm110)
REVERT: A  449 MET cc_start: 0.8074 (ttp) cc_final: 0.7736 (ttt)
REVERT: B   39 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7255 (mtp180)
REVERT: B  165 LYS cc_start: 0.8055 (pttt) cc_final: 0.7413 (ptmm)
REVERT: B  258 MET cc_start: 0.8110 (ttp) cc_final: 0.7848 (ttt)
REVERT: C   39 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7374 (mtp180)
REVERT: C  165 LYS cc_start: 0.8139 (pttt) cc_final: 0.7534 (ptmm)
REVERT: C  258 MET cc_start: 0.8151 (ttp) cc_final: 0.7821 (ttt)
REVERT: C  315 ARG cc_start: 0.7612 (mpt-90) cc_final: 0.7067 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7370 (ttm110)
REVERT: C  449 MET cc_start: 0.7923 (ttp) cc_final: 0.7625 (ttt)
  outliers start: 19
  outliers final: 16
  residues processed: 151
  average time/residue: 0.2442
  time to fit residues: 50.8067
Evaluate side-chains
  156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  391 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  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 54 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 118 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.150751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.101234 restraints weight = 11139.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.88
r_work: 0.2765 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2597 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    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 = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10497  Z= 0.104
  Angle     :  0.475   9.063  14175  Z= 0.241
  Chirality :  0.037   0.123   1767
  Planarity :  0.003   0.027   1677
  Dihedral  :  8.784  68.110   2064
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.31 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.25), residues: 1272
  helix:  1.96 (0.18), residues: 939
  sheet: -0.86 (0.73), residues: 60
  loop : -0.97 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  19 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.007   0.001   PHE C 159 
 TYR   0.017   0.001   TYR C 206 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  708)
  hydrogen bonds       : angle       3.63192 ( 2079)
  covalent geometry    : bond        0.00226 (10497)
  covalent geometry    : angle       0.47504 (14175)

*********************** 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
  163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8883 (mmt) cc_final: 0.8567 (mmm)
REVERT: A  165 LYS cc_start: 0.8064 (pttt) cc_final: 0.7390 (ptmm)
REVERT: A  255 MET cc_start: 0.8708 (mmm) cc_final: 0.8393 (mmm)
REVERT: A  258 MET cc_start: 0.8096 (ttp) cc_final: 0.7714 (ttt)
REVERT: A  353 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7427 (ttm110)
REVERT: A  449 MET cc_start: 0.8046 (ttp) cc_final: 0.7713 (ttt)
REVERT: B   39 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7239 (mtp180)
REVERT: B  165 LYS cc_start: 0.8029 (pttt) cc_final: 0.7387 (ptmm)
REVERT: B  258 MET cc_start: 0.8056 (ttp) cc_final: 0.7793 (ttt)
REVERT: C   39 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7348 (mtp180)
REVERT: C  165 LYS cc_start: 0.8110 (pttt) cc_final: 0.7508 (ptmm)
REVERT: C  258 MET cc_start: 0.8093 (ttp) cc_final: 0.7763 (ttt)
REVERT: C  315 ARG cc_start: 0.7584 (mpt-90) cc_final: 0.7036 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7400 (ttm110)
  outliers start: 17
  outliers final: 12
  residues processed: 156
  average time/residue: 0.2733
  time to fit residues: 60.6403
Evaluate side-chains
  155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
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   48 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 7 optimal weight:    0.0270
   chunk 97 optimal weight:    7.9990
   chunk 111 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0470
   chunk 32 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.152768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.103333 restraints weight = 11553.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.89
r_work: 0.2796 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10497  Z= 0.095
  Angle     :  0.468   9.352  14175  Z= 0.239
  Chirality :  0.037   0.121   1767
  Planarity :  0.003   0.026   1677
  Dihedral  :  8.465  65.409   2064
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.88 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.25), residues: 1272
  helix:  2.18 (0.18), residues: 924
  sheet: -0.88 (0.73), residues: 60
  loop : -1.16 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  19 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.007   0.001   PHE A 159 
 TYR   0.016   0.001   TYR A 206 
 ARG   0.001   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  708)
  hydrogen bonds       : angle       3.60006 ( 2079)
  covalent geometry    : bond        0.00190 (10497)
  covalent geometry    : angle       0.46811 (14175)

*********************** 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
  158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 2.479 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8607 (mmt) cc_final: 0.8374 (mmm)
REVERT: A  165 LYS cc_start: 0.8019 (pttt) cc_final: 0.7413 (ptmm)
REVERT: A  255 MET cc_start: 0.8595 (mmm) cc_final: 0.8295 (mmm)
REVERT: A  258 MET cc_start: 0.7932 (ttp) cc_final: 0.7551 (ttt)
REVERT: A  449 MET cc_start: 0.7902 (ttp) cc_final: 0.7556 (ttt)
REVERT: B   39 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7269 (mtp180)
REVERT: B  165 LYS cc_start: 0.8050 (pttt) cc_final: 0.7421 (ptmm)
REVERT: B  258 MET cc_start: 0.7895 (ttp) cc_final: 0.7644 (ttt)
REVERT: C   39 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7318 (mtp180)
REVERT: C  142 MET cc_start: 0.7870 (mtm) cc_final: 0.7634 (mtp)
REVERT: C  165 LYS cc_start: 0.8073 (pttt) cc_final: 0.7483 (ptmm)
REVERT: C  258 MET cc_start: 0.7898 (ttp) cc_final: 0.7593 (ttt)
REVERT: C  315 ARG cc_start: 0.7542 (mpt-90) cc_final: 0.7031 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7452 (ttm110)
  outliers start: 15
  outliers final: 10
  residues processed: 152
  average time/residue: 0.3609
  time to fit residues: 80.0177
Evaluate side-chains
  148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 1.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 125 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0670
   chunk 15 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3597 r_free = 0.3597 target = 0.152147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.102335 restraints weight = 11394.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.90
r_work: 0.2787 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10497  Z= 0.101
  Angle     :  0.479   9.291  14175  Z= 0.243
  Chirality :  0.037   0.121   1767
  Planarity :  0.003   0.026   1677
  Dihedral  :  8.392  64.590   2064
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.26 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.25), residues: 1272
  helix:  2.19 (0.18), residues: 924
  sheet: -0.89 (0.73), residues: 60
  loop : -1.12 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 441 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.008   0.001   PHE A 159 
 TYR   0.012   0.001   TYR C 206 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  708)
  hydrogen bonds       : angle       3.63264 ( 2079)
  covalent geometry    : bond        0.00217 (10497)
  covalent geometry    : angle       0.47875 (14175)

*********************** 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
  146 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 1.263 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8597 (mmt) cc_final: 0.8383 (mmm)
REVERT: A  165 LYS cc_start: 0.8042 (pttt) cc_final: 0.7430 (ptmm)
REVERT: A  255 MET cc_start: 0.8633 (mmm) cc_final: 0.8321 (mmm)
REVERT: A  258 MET cc_start: 0.7941 (ttp) cc_final: 0.7550 (ttt)
REVERT: A  449 MET cc_start: 0.7832 (ttp) cc_final: 0.7478 (ttt)
REVERT: B   39 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7338 (mtp180)
REVERT: B  165 LYS cc_start: 0.8024 (pttt) cc_final: 0.7410 (ptmm)
REVERT: B  258 MET cc_start: 0.7883 (ttp) cc_final: 0.7641 (ttt)
REVERT: C   39 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7330 (mtp180)
REVERT: C  142 MET cc_start: 0.7883 (mtm) cc_final: 0.7659 (mtp)
REVERT: C  165 LYS cc_start: 0.8070 (pttt) cc_final: 0.7496 (ptmm)
REVERT: C  255 MET cc_start: 0.8699 (mmm) cc_final: 0.8409 (mmm)
REVERT: C  258 MET cc_start: 0.7954 (ttp) cc_final: 0.7608 (ttt)
REVERT: C  315 ARG cc_start: 0.7540 (mpt-90) cc_final: 0.7027 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7461 (ttm110)
REVERT: C  449 MET cc_start: 0.7760 (ttp) cc_final: 0.7340 (ttp)
  outliers start: 11
  outliers final: 11
  residues processed: 139
  average time/residue: 0.3128
  time to fit residues: 62.0411
Evaluate side-chains
  145 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 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  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  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 95 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 29 optimal weight:    7.9990
   chunk 116 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.152025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.102346 restraints weight = 11240.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.88
r_work: 0.2782 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056  10497  Z= 0.104
  Angle     :  0.484   9.101  14175  Z= 0.246
  Chirality :  0.037   0.134   1767
  Planarity :  0.003   0.026   1677
  Dihedral  :  8.354  63.905   2064
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.45 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.25), residues: 1272
  helix:  2.20 (0.18), residues: 924
  sheet: -0.92 (0.72), residues: 60
  loop : -1.07 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 441 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.008   0.001   PHE A 159 
 TYR   0.011   0.001   TYR C 206 
 ARG   0.001   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  708)
  hydrogen bonds       : angle       3.65319 ( 2079)
  covalent geometry    : bond        0.00228 (10497)
  covalent geometry    : angle       0.48394 (14175)

********************** 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
  149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8602 (mmt) cc_final: 0.8365 (mmm)
REVERT: A  165 LYS cc_start: 0.8034 (pttt) cc_final: 0.7413 (ptmm)
REVERT: A  255 MET cc_start: 0.8618 (mmm) cc_final: 0.8300 (mmm)
REVERT: A  258 MET cc_start: 0.7940 (ttp) cc_final: 0.7548 (ttt)
REVERT: A  353 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7456 (ttm110)
REVERT: A  356 ARG cc_start: 0.8356 (ttm170) cc_final: 0.8135 (mtm-85)
REVERT: A  449 MET cc_start: 0.7862 (ttp) cc_final: 0.7515 (ttt)
REVERT: B   39 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7329 (mtp180)
REVERT: B  165 LYS cc_start: 0.8019 (pttt) cc_final: 0.7400 (ptmm)
REVERT: B  255 MET cc_start: 0.8496 (mmm) cc_final: 0.8190 (mmm)
REVERT: B  258 MET cc_start: 0.7881 (ttp) cc_final: 0.7632 (ttt)
REVERT: C   39 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7316 (mtp180)
REVERT: C  142 MET cc_start: 0.7851 (mtm) cc_final: 0.7635 (mtp)
REVERT: C  165 LYS cc_start: 0.8026 (pttt) cc_final: 0.7445 (ptmm)
REVERT: C  255 MET cc_start: 0.8661 (mmm) cc_final: 0.8349 (mmm)
REVERT: C  258 MET cc_start: 0.7880 (ttp) cc_final: 0.7524 (ttt)
REVERT: C  315 ARG cc_start: 0.7534 (mpt-90) cc_final: 0.7024 (tpp-160)
REVERT: C  353 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7463 (ttm110)
REVERT: C  449 MET cc_start: 0.7739 (ttp) cc_final: 0.7313 (ttp)
  outliers start: 11
  outliers final: 8
  residues processed: 142
  average time/residue: 0.3104
  time to fit residues: 60.4141
Evaluate side-chains
  147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  270 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 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 116 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.152221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.101935 restraints weight = 11690.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.93
r_work: 0.2775 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067  10497  Z= 0.105
  Angle     :  0.485   9.169  14175  Z= 0.247
  Chirality :  0.037   0.175   1767
  Planarity :  0.003   0.026   1677
  Dihedral  :  8.329  63.372   2064
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 14.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1272
  helix:  2.20 (0.18), residues: 924
  sheet: -0.97 (0.71), residues: 60
  loop : -1.02 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 441 
 HIS   0.000   0.000   HIS B 296 
 PHE   0.008   0.001   PHE A 159 
 TYR   0.011   0.001   TYR C 206 
 ARG   0.001   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  708)
  hydrogen bonds       : angle       3.66758 ( 2079)
  covalent geometry    : bond        0.00234 (10497)
  covalent geometry    : angle       0.48532 (14175)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6826.83 seconds
wall clock time: 125 minutes 28.06 seconds (7528.06 seconds total)