Starting phenix.real_space_refine
on Mon Jul 28 13:43:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7npw_12524/07_2025/7npw_12524.cif"
  }
  resolution = 3.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 732 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    6381      2.51       5
     N    1569      2.21       5
     O    1713      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 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: 9723
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3241
          Classifications: {'peptide': 426}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 15, 'TRANS': 410}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.69, per 1000 atoms: 0.69
  Number of scatterers: 9723
  At special positions: 0
  Unit cell: (126.17, 121.286, 83.842, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1713      8.00
     N    1569      7.00
     C    6381      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: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      81.3% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 36
      removed outlier: 3.556A  pdb=" N   VAL A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 48
    Processing helix  chain 'A' and resid 48 through 69
      removed outlier: 3.767A  pdb=" N   LEU A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 115
      Proline residue:  A  84  - end of helix
      removed outlier: 4.932A  pdb=" N   LEU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      Proline residue:  A  98  - end of helix
      removed outlier: 3.723A  pdb=" N   ASP A 112 " --> pdb=" O   MET A 108 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER A 113 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 146
      removed outlier: 3.762A  pdb=" N   MET A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.864A  pdb=" N   PHE A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 259
      removed outlier: 3.555A  pdb=" N   LEU A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 286
      removed outlier: 3.650A  pdb=" N   PHE A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 304
      removed outlier: 3.670A  pdb=" N   VAL A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 303 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 331
      removed outlier: 3.747A  pdb=" N   ILE A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 341
      removed outlier: 3.550A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 363
      removed outlier: 3.820A  pdb=" N   PHE A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLN A 354 " --> pdb=" O   GLY A 350 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   ALA A 355 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 386 through 397
      removed outlier: 3.547A  pdb=" N   VAL A 390 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU A 391 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 402 through 417
      removed outlier: 3.720A  pdb=" N   ASN A 417 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.896A  pdb=" N   THR A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 459
    Processing helix  chain 'A' and resid 464 through 470
      removed outlier: 4.027A  pdb=" N   ILE A 468 " --> pdb=" O   ASP A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 497
      removed outlier: 3.521A  pdb=" N   LEU A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 477 " --> pdb=" O   TRP A 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 36
    Processing helix  chain 'B' and resid 41 through 48
    Processing helix  chain 'B' and resid 48 through 69
      removed outlier: 3.768A  pdb=" N   LEU B  52 " --> pdb=" O   ASN B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 115
      Proline residue:  B  84  - end of helix
      removed outlier: 4.931A  pdb=" N   LEU B  97 " --> pdb=" O   GLN B  93 " (cutoff:3.500A)
      Proline residue:  B  98  - end of helix
      removed outlier: 3.724A  pdb=" N   ASP B 112 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER B 113 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 146
      removed outlier: 3.762A  pdb=" N   MET B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 177
    Processing helix  chain 'B' and resid 181 through 187
      removed outlier: 3.865A  pdb=" N   PHE B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 259
      removed outlier: 3.556A  pdb=" N   LEU B 246 " --> pdb=" O   ASN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 286
      removed outlier: 3.651A  pdb=" N   PHE B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 304
      removed outlier: 3.669A  pdb=" N   VAL B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU B 303 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 331
      removed outlier: 3.747A  pdb=" N   ILE B 310 " --> pdb=" O   ASP B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 341
      removed outlier: 3.550A  pdb=" N   VAL B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 363
      removed outlier: 3.819A  pdb=" N   PHE B 348 " --> pdb=" O   ASN B 344 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLN B 354 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   ALA B 355 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
    Processing helix  chain 'B' and resid 386 through 397
      removed outlier: 3.546A  pdb=" N   VAL B 390 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU B 391 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      Proline residue:  B 392  - end of helix
    Processing helix  chain 'B' and resid 402 through 417
      removed outlier: 3.719A  pdb=" N   ASN B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 437
      removed outlier: 3.897A  pdb=" N   THR B 428 " --> pdb=" O   GLY B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 459
    Processing helix  chain 'B' and resid 464 through 470
      removed outlier: 4.026A  pdb=" N   ILE B 468 " --> pdb=" O   ASP B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 497
      removed outlier: 3.520A  pdb=" N   LEU B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 477 " --> pdb=" O   TRP B 473 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 41 through 48
    Processing helix  chain 'C' and resid 48 through 69
      removed outlier: 3.767A  pdb=" N   LEU C  52 " --> pdb=" O   ASN C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 115
      Proline residue:  C  84  - end of helix
      removed outlier: 4.931A  pdb=" N   LEU C  97 " --> pdb=" O   GLN C  93 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
      removed outlier: 3.723A  pdb=" N   ASP C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   SER C 113 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 146
      removed outlier: 3.762A  pdb=" N   MET C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 177
    Processing helix  chain 'C' and resid 181 through 187
      removed outlier: 3.865A  pdb=" N   PHE C 187 " --> pdb=" O   VAL C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 259
      removed outlier: 3.555A  pdb=" N   LEU C 246 " --> pdb=" O   ASN C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 286
      removed outlier: 3.651A  pdb=" N   PHE C 270 " --> pdb=" O   ALA C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 304
      removed outlier: 3.669A  pdb=" N   VAL C 302 " --> pdb=" O   ALA C 298 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU C 303 " --> pdb=" O   GLY C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 331
      removed outlier: 3.747A  pdb=" N   ILE C 310 " --> pdb=" O   ASP C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 341
      removed outlier: 3.550A  pdb=" N   VAL C 340 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 363
      removed outlier: 3.820A  pdb=" N   PHE C 348 " --> pdb=" O   ASN C 344 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLN C 354 " --> pdb=" O   GLY C 350 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   ALA C 355 " --> pdb=" O   GLY C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 379
    Processing helix  chain 'C' and resid 386 through 397
      removed outlier: 3.547A  pdb=" N   VAL C 390 " --> pdb=" O   VAL C 386 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU C 391 " --> pdb=" O   THR C 387 " (cutoff:3.500A)
      Proline residue:  C 392  - end of helix
    Processing helix  chain 'C' and resid 402 through 417
      removed outlier: 3.720A  pdb=" N   ASN C 417 " --> pdb=" O   ILE C 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 437
      removed outlier: 3.897A  pdb=" N   THR C 428 " --> pdb=" O   GLY C 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 446 through 459
    Processing helix  chain 'C' and resid 464 through 470
      removed outlier: 4.025A  pdb=" N   ILE C 468 " --> pdb=" O   ASP C 464 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 497
      removed outlier: 3.520A  pdb=" N   LEU C 475 " --> pdb=" O   VAL C 471 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG C 477 " --> pdb=" O   TRP C 473 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.516A  pdb=" N   VAL A 238 " --> pdb=" O   GLN A 189 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 190
      removed outlier: 3.517A  pdb=" N   VAL B 238 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 190
      removed outlier: 3.517A  pdb=" N   VAL C 238 " --> pdb=" O   GLN C 189 " (cutoff:3.500A)

    708 hydrogen bonds defined for protein.
    2124 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: 2.63

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3018
        1.34 -     1.46: 1839
        1.46 -     1.58: 4917
        1.58 -     1.70: 0
        1.70 -     1.81: 111
  Bond restraints: 9885
  Sorted by residual:
  bond pdb=" C   ALA C 289 "
       pdb=" N   PRO C 290 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 8.64e-01
  bond pdb=" C   ALA B 289 "
       pdb=" N   PRO B 290 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.39e-01
  bond pdb=" C   ALA A 289 "
       pdb=" N   PRO A 290 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.19e-01
  bond pdb=" CA  GLN B  93 "
       pdb=" CB  GLN B  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.015 1.75e-02 3.27e+03 7.81e-01
  bond pdb=" CA  GLN A  93 "
       pdb=" CB  GLN A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.015 1.75e-02 3.27e+03 7.66e-01
  ... (remaining 9880 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 12920
        1.50 -     3.00: 392
        3.00 -     4.50: 74
        4.50 -     6.00: 33
        6.00 -     7.51: 9
  Bond angle restraints: 13428
  Sorted by residual:
  angle pdb=" C   ILE A 469 "
        pdb=" CA  ILE A 469 "
        pdb=" CB  ILE A 469 "
      ideal   model   delta    sigma   weight residual
     111.37  107.02    4.35 1.68e+00 3.54e-01 6.71e+00
  angle pdb=" C   ILE C 469 "
        pdb=" CA  ILE C 469 "
        pdb=" CB  ILE C 469 "
      ideal   model   delta    sigma   weight residual
     111.37  107.06    4.31 1.68e+00 3.54e-01 6.57e+00
  angle pdb=" C   ILE B 469 "
        pdb=" CA  ILE B 469 "
        pdb=" CB  ILE B 469 "
      ideal   model   delta    sigma   weight residual
     111.37  107.09    4.28 1.68e+00 3.54e-01 6.50e+00
  angle pdb=" CB  MET B  89 "
        pdb=" CG  MET B  89 "
        pdb=" SD  MET B  89 "
      ideal   model   delta    sigma   weight residual
     112.70  120.21   -7.51 3.00e+00 1.11e-01 6.26e+00
  angle pdb=" CB  MET A  89 "
        pdb=" CG  MET A  89 "
        pdb=" SD  MET A  89 "
      ideal   model   delta    sigma   weight residual
     112.70  120.19   -7.49 3.00e+00 1.11e-01 6.23e+00
  ... (remaining 13423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 5373
       18.00 -    35.99: 411
       35.99 -    53.99: 72
       53.99 -    71.99: 12
       71.99 -    89.98: 9
  Dihedral angle restraints: 5877
    sinusoidal: 2226
      harmonic: 3651
  Sorted by residual:
  dihedral pdb=" CA  GLN B  93 "
           pdb=" C   GLN B  93 "
           pdb=" N   MET B  94 "
           pdb=" CA  MET B  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.70   22.30     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  GLN C  93 "
           pdb=" C   GLN C  93 "
           pdb=" N   MET C  94 "
           pdb=" CA  MET C  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  GLN A  93 "
           pdb=" C   GLN A  93 "
           pdb=" N   MET A  94 "
           pdb=" CA  MET A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 5874 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 960
       0.028 -    0.056: 445
       0.056 -    0.085: 191
       0.085 -    0.113: 81
       0.113 -    0.141: 12
  Chirality restraints: 1689
  Sorted by residual:
  chirality pdb=" CB  VAL A 471 "
            pdb=" CA  VAL A 471 "
            pdb=" CG1 VAL A 471 "
            pdb=" CG2 VAL A 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CB  VAL B 471 "
            pdb=" CA  VAL B 471 "
            pdb=" CG1 VAL B 471 "
            pdb=" CG2 VAL B 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CB  VAL C 471 "
            pdb=" CA  VAL C 471 "
            pdb=" CG1 VAL C 471 "
            pdb=" CG2 VAL C 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 1686 not shown)

  Planarity restraints: 1641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 373 "   -0.010 2.00e-02 2.50e+03   9.92e-03 1.72e+00
        pdb=" CG  PHE A 373 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 373 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 373 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 373 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 373 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 373 "   -0.010 2.00e-02 2.50e+03   9.91e-03 1.72e+00
        pdb=" CG  PHE B 373 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 373 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 373 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 373 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 373 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 373 "   -0.010 2.00e-02 2.50e+03   9.70e-03 1.65e+00
        pdb=" CG  PHE C 373 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 373 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 373 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 373 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 373 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1638 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2577
        2.81 -     3.33: 10837
        3.33 -     3.86: 16117
        3.86 -     4.38: 17040
        4.38 -     4.90: 29648
  Nonbonded interactions: 76219
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 384 "
            pdb=" NH1 ARG A 388 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   LYS B 384 "
            pdb=" NH1 ARG B 388 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   LYS C 384 "
            pdb=" NH1 ARG C 388 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   LEU B 369 "
            pdb=" OG1 THR B 372 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   LEU A 369 "
            pdb=" OG1 THR A 372 "
     model   vdw
     2.295 3.040
  ... (remaining 76214 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             50.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.610
  Find NCS groups from input model:        0.190
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   79.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
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      :  0.003   0.022   9885  Z= 0.129
  Angle     :  0.673   7.505  13428  Z= 0.354
  Chirality :  0.041   0.141   1689
  Planarity :  0.004   0.030   1641
  Dihedral  : 13.765  89.984   3525
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  0.92 (0.24), residues: 1254
  helix:  1.46 (0.17), residues: 945
  sheet: -1.52 (0.79), residues: 48
  loop : -2.10 (0.33), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C 346 
 HIS   0.001   0.000   HIS C 328 
 PHE   0.023   0.001   PHE A 373 
 TYR   0.017   0.001   TYR C 405 
 ARG   0.011   0.001   ARG B 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10638 (  708)
  hydrogen bonds       : angle       4.74206 ( 2124)
  covalent geometry    : bond        0.00250 ( 9885)
  covalent geometry    : angle       0.67275 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8711 (m-10) cc_final: 0.8231 (t80)
REVERT: A  288 TYR cc_start: 0.9215 (t80) cc_final: 0.8787 (t80)
REVERT: A  451 MET cc_start: 0.9204 (mmp) cc_final: 0.8754 (mmp)
REVERT: A  476 ASP cc_start: 0.7474 (m-30) cc_final: 0.7077 (t0)
REVERT: B   80 TYR cc_start: 0.8565 (m-10) cc_final: 0.8080 (t80)
REVERT: B  189 GLN cc_start: 0.7050 (mp-120) cc_final: 0.6827 (mp10)
REVERT: B  288 TYR cc_start: 0.9303 (t80) cc_final: 0.9002 (t80)
REVERT: B  451 MET cc_start: 0.9069 (mmp) cc_final: 0.8611 (mmp)
REVERT: C   80 TYR cc_start: 0.8669 (m-10) cc_final: 0.8027 (t80)
REVERT: C  108 MET cc_start: 0.9013 (mmm) cc_final: 0.8619 (tpp)
REVERT: C  251 MET cc_start: 0.8225 (mtp) cc_final: 0.7982 (tmm)
REVERT: C  307 MET cc_start: 0.6234 (tmm) cc_final: 0.6021 (tmm)
REVERT: C  451 MET cc_start: 0.9136 (mmp) cc_final: 0.8645 (mmp)
REVERT: C  476 ASP cc_start: 0.7366 (m-30) cc_final: 0.7049 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1791
  time to fit residues: 68.5848
Evaluate side-chains
  203 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:   20.0000
   chunk 114 optimal weight:    9.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.103260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.075047 restraints weight = 35095.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.077457 restraints weight = 17451.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.079050 restraints weight = 11208.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9885  Z= 0.128
  Angle     :  0.616  10.264  13428  Z= 0.311
  Chirality :  0.040   0.130   1689
  Planarity :  0.004   0.029   1641
  Dihedral  :  3.850  19.114   1344
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.02 %
    Favored  : 83.33 %
  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:  0.99 (0.24), residues: 1254
  helix:  1.45 (0.16), residues: 975
  sheet: -1.46 (0.82), residues: 48
  loop : -2.25 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 473 
 HIS   0.000   0.000   HIS A 328 
 PHE   0.016   0.001   PHE B  83 
 TYR   0.020   0.001   TYR B  75 
 ARG   0.007   0.001   ARG C 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  708)
  hydrogen bonds       : angle       4.01870 ( 2124)
  covalent geometry    : bond        0.00278 ( 9885)
  covalent geometry    : angle       0.61610 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 217
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8666 (m-10) cc_final: 0.8230 (t80)
REVERT: A  177 MET cc_start: 0.8707 (ttp) cc_final: 0.8167 (ttm)
REVERT: A  288 TYR cc_start: 0.9078 (t80) cc_final: 0.8839 (t80)
REVERT: A  336 LEU cc_start: 0.8577 (tt) cc_final: 0.8219 (pp)
REVERT: A  451 MET cc_start: 0.8994 (mmp) cc_final: 0.8550 (mmp)
REVERT: B   80 TYR cc_start: 0.8647 (m-10) cc_final: 0.8194 (t80)
REVERT: B  288 TYR cc_start: 0.9160 (t80) cc_final: 0.8907 (t80)
REVERT: B  316 MET cc_start: 0.9344 (mmm) cc_final: 0.9125 (mmm)
REVERT: B  405 TYR cc_start: 0.8952 (t80) cc_final: 0.8599 (t80)
REVERT: B  451 MET cc_start: 0.8906 (mmp) cc_final: 0.8250 (mmp)
REVERT: C   80 TYR cc_start: 0.8723 (m-10) cc_final: 0.8157 (t80)
REVERT: C  108 MET cc_start: 0.8988 (mmm) cc_final: 0.8641 (tpp)
REVERT: C  177 MET cc_start: 0.8645 (mtt) cc_final: 0.8281 (ttp)
REVERT: C  286 MET cc_start: 0.9097 (mmp) cc_final: 0.8714 (tpp)
REVERT: C  307 MET cc_start: 0.6508 (tmm) cc_final: 0.6005 (tmm)
REVERT: C  316 MET cc_start: 0.9231 (mmm) cc_final: 0.9006 (mmm)
REVERT: C  336 LEU cc_start: 0.8525 (tt) cc_final: 0.8260 (pp)
REVERT: C  451 MET cc_start: 0.8993 (mmp) cc_final: 0.8502 (mmp)
  outliers start: 28
  outliers final: 22
  residues processed: 230
  average time/residue: 0.1867
  time to fit residues: 63.7615
Evaluate side-chains
  222 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   66 PHE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.098885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.071267 restraints weight = 35441.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.073289 restraints weight = 19546.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.074591 restraints weight = 13025.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9885  Z= 0.198
  Angle     :  0.655  10.287  13428  Z= 0.340
  Chirality :  0.041   0.154   1689
  Planarity :  0.005   0.039   1641
  Dihedral  :  4.078  19.002   1344
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.41 %
    Favored  : 77.18 %
  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 (0.23), residues: 1254
  helix:  1.29 (0.16), residues: 984
  sheet: -1.44 (0.81), residues: 48
  loop : -2.06 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 287 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.020   0.002   PHE B 170 
 TYR   0.023   0.002   TYR C 288 
 ARG   0.007   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  708)
  hydrogen bonds       : angle       4.13054 ( 2124)
  covalent geometry    : bond        0.00434 ( 9885)
  covalent geometry    : angle       0.65516 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 188
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8705 (m-10) cc_final: 0.8402 (t80)
REVERT: A  242 ASN cc_start: 0.8923 (t0) cc_final: 0.8669 (t0)
REVERT: A  336 LEU cc_start: 0.8878 (tt) cc_final: 0.8651 (pp)
REVERT: A  451 MET cc_start: 0.8834 (mmp) cc_final: 0.8371 (mmp)
REVERT: A  476 ASP cc_start: 0.8027 (m-30) cc_final: 0.7262 (p0)
REVERT: B   80 TYR cc_start: 0.8639 (m-10) cc_final: 0.8398 (t80)
REVERT: B   88 LEU cc_start: 0.9804 (tt) cc_final: 0.9597 (tt)
REVERT: B  242 ASN cc_start: 0.9040 (t0) cc_final: 0.8741 (t0)
REVERT: B  451 MET cc_start: 0.8809 (mmp) cc_final: 0.8300 (mmp)
REVERT: C   80 TYR cc_start: 0.8659 (m-10) cc_final: 0.8355 (t80)
REVERT: C   88 LEU cc_start: 0.9763 (tt) cc_final: 0.9458 (tt)
REVERT: C  108 MET cc_start: 0.8916 (mmm) cc_final: 0.8667 (tpp)
REVERT: C  171 LEU cc_start: 0.9513 (tp) cc_final: 0.9270 (tp)
REVERT: C  242 ASN cc_start: 0.8898 (t0) cc_final: 0.8601 (t0)
REVERT: C  286 MET cc_start: 0.9050 (mmp) cc_final: 0.8779 (tpt)
REVERT: C  316 MET cc_start: 0.9352 (mmm) cc_final: 0.9111 (mmm)
REVERT: C  336 LEU cc_start: 0.8799 (tt) cc_final: 0.8522 (pp)
REVERT: C  405 TYR cc_start: 0.9156 (t80) cc_final: 0.8777 (t80)
REVERT: C  451 MET cc_start: 0.8858 (mmp) cc_final: 0.8138 (mmp)
REVERT: C  476 ASP cc_start: 0.7829 (m-30) cc_final: 0.7168 (p0)
  outliers start: 36
  outliers final: 27
  residues processed: 210
  average time/residue: 0.2172
  time to fit residues: 68.5494
Evaluate side-chains
  194 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  252 CYS
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0570
   chunk 52 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   chunk 18 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.102626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074870 restraints weight = 35011.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.077037 restraints weight = 18234.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.078457 restraints weight = 12097.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9885  Z= 0.117
  Angle     :  0.621  11.000  13428  Z= 0.310
  Chirality :  0.041   0.185   1689
  Planarity :  0.004   0.033   1641
  Dihedral  :  3.840  19.570   1344
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.50 %
    Favored  : 75.09 %
  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:  1.02 (0.24), residues: 1254
  helix:  1.43 (0.16), residues: 975
  sheet: -1.64 (0.79), residues: 48
  loop : -2.04 (0.36), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 346 
 HIS   0.001   0.000   HIS A 328 
 PHE   0.021   0.001   PHE B  83 
 TYR   0.025   0.001   TYR A 288 
 ARG   0.002   0.000   ARG A 388 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  708)
  hydrogen bonds       : angle       3.92283 ( 2124)
  covalent geometry    : bond        0.00250 ( 9885)
  covalent geometry    : angle       0.62135 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 206
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8669 (m-10) cc_final: 0.8352 (t80)
REVERT: A  242 ASN cc_start: 0.8820 (t0) cc_final: 0.8551 (t0)
REVERT: A  336 LEU cc_start: 0.8864 (tt) cc_final: 0.8570 (pp)
REVERT: A  451 MET cc_start: 0.8781 (mmp) cc_final: 0.8298 (mmp)
REVERT: A  476 ASP cc_start: 0.7858 (m-30) cc_final: 0.7275 (p0)
REVERT: B   80 TYR cc_start: 0.8598 (m-10) cc_final: 0.8334 (t80)
REVERT: B   93 GLN cc_start: 0.8512 (pp30) cc_final: 0.7950 (pp30)
REVERT: B   94 MET cc_start: 0.8966 (ttm) cc_final: 0.8687 (ttm)
REVERT: B  177 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8261 (ttp)
REVERT: B  405 TYR cc_start: 0.9028 (t80) cc_final: 0.8568 (t80)
REVERT: B  451 MET cc_start: 0.8774 (mmp) cc_final: 0.8004 (mmp)
REVERT: C   80 TYR cc_start: 0.8730 (m-10) cc_final: 0.8345 (t80)
REVERT: C   83 PHE cc_start: 0.8371 (t80) cc_final: 0.8041 (t80)
REVERT: C  177 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (ttp)
REVERT: C  242 ASN cc_start: 0.8702 (t0) cc_final: 0.8485 (t0)
REVERT: C  251 MET cc_start: 0.7895 (tmm) cc_final: 0.7490 (tmm)
REVERT: C  316 MET cc_start: 0.9365 (mmm) cc_final: 0.9153 (mmm)
REVERT: C  336 LEU cc_start: 0.8880 (tt) cc_final: 0.8560 (pp)
REVERT: C  405 TYR cc_start: 0.9074 (t80) cc_final: 0.8637 (t80)
REVERT: C  451 MET cc_start: 0.8863 (mmp) cc_final: 0.8070 (mmp)
REVERT: C  476 ASP cc_start: 0.7742 (m-30) cc_final: 0.7193 (p0)
  outliers start: 36
  outliers final: 23
  residues processed: 226
  average time/residue: 0.2095
  time to fit residues: 70.5341
Evaluate side-chains
  205 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  448 LEU
Chi-restraints excluded: chain C residue  464 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 108 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 114 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.098643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.070949 restraints weight = 34949.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.073050 restraints weight = 18237.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.074387 restraints weight = 12077.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9885  Z= 0.182
  Angle     :  0.649   9.282  13428  Z= 0.335
  Chirality :  0.041   0.173   1689
  Planarity :  0.004   0.039   1641
  Dihedral  :  4.038  21.264   1344
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.48 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.23), residues: 1254
  helix:  1.36 (0.16), residues: 978
  sheet: -1.70 (0.80), residues: 48
  loop : -1.89 (0.36), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 287 
 HIS   0.002   0.001   HIS C 328 
 PHE   0.022   0.002   PHE B  83 
 TYR   0.022   0.002   TYR A 317 
 ARG   0.003   0.001   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  708)
  hydrogen bonds       : angle       4.07151 ( 2124)
  covalent geometry    : bond        0.00405 ( 9885)
  covalent geometry    : angle       0.64884 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 195
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8659 (m-10) cc_final: 0.8370 (t80)
REVERT: A   93 GLN cc_start: 0.8620 (pp30) cc_final: 0.7951 (pp30)
REVERT: A  242 ASN cc_start: 0.8878 (t0) cc_final: 0.8659 (t0)
REVERT: A  304 MET cc_start: 0.9220 (tmm) cc_final: 0.8736 (tmm)
REVERT: A  336 LEU cc_start: 0.9041 (tt) cc_final: 0.8744 (pp)
REVERT: A  451 MET cc_start: 0.8836 (mmp) cc_final: 0.8418 (mmp)
REVERT: A  476 ASP cc_start: 0.8005 (m-30) cc_final: 0.7261 (p0)
REVERT: B   88 LEU cc_start: 0.9759 (tt) cc_final: 0.9540 (tt)
REVERT: B   93 GLN cc_start: 0.8664 (pp30) cc_final: 0.8255 (pp30)
REVERT: B  316 MET cc_start: 0.9436 (mmm) cc_final: 0.9199 (mmm)
REVERT: B  451 MET cc_start: 0.8832 (mmp) cc_final: 0.8233 (mmp)
REVERT: C   83 PHE cc_start: 0.8617 (t80) cc_final: 0.8248 (t80)
REVERT: C   93 GLN cc_start: 0.8728 (pp30) cc_final: 0.8377 (pp30)
REVERT: C   94 MET cc_start: 0.9036 (ttm) cc_final: 0.8808 (ttm)
REVERT: C  171 LEU cc_start: 0.9470 (tp) cc_final: 0.9244 (tp)
REVERT: C  336 LEU cc_start: 0.8984 (tt) cc_final: 0.8620 (pp)
REVERT: C  405 TYR cc_start: 0.9166 (t80) cc_final: 0.8774 (t80)
REVERT: C  451 MET cc_start: 0.8840 (mmp) cc_final: 0.8085 (mmp)
REVERT: C  476 ASP cc_start: 0.7845 (m-30) cc_final: 0.7219 (p0)
  outliers start: 44
  outliers final: 30
  residues processed: 224
  average time/residue: 0.2469
  time to fit residues: 82.9497
Evaluate side-chains
  210 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 180
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.102144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.075242 restraints weight = 34422.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.077322 restraints weight = 18161.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.078586 restraints weight = 12085.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9885  Z= 0.152
  Angle     :  0.667  11.967  13428  Z= 0.333
  Chirality :  0.041   0.159   1689
  Planarity :  0.004   0.036   1641
  Dihedral  :  4.028  20.157   1344
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.53 %
    Favored  : 71.69 %
  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:  0.94 (0.23), residues: 1254
  helix:  1.33 (0.16), residues: 984
  sheet: -1.69 (0.79), residues: 48
  loop : -1.92 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 473 
 HIS   0.002   0.000   HIS A 328 
 PHE   0.020   0.001   PHE B  83 
 TYR   0.021   0.002   TYR A 288 
 ARG   0.003   0.000   ARG C 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  708)
  hydrogen bonds       : angle       4.02818 ( 2124)
  covalent geometry    : bond        0.00345 ( 9885)
  covalent geometry    : angle       0.66728 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 213
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8759 (pp30) cc_final: 0.7999 (pp30)
REVERT: A  304 MET cc_start: 0.9017 (tmm) cc_final: 0.8627 (tmm)
REVERT: A  336 LEU cc_start: 0.9075 (tt) cc_final: 0.8849 (pp)
REVERT: A  405 TYR cc_start: 0.9006 (t80) cc_final: 0.8515 (t80)
REVERT: A  451 MET cc_start: 0.8678 (mmp) cc_final: 0.7961 (mmp)
REVERT: A  476 ASP cc_start: 0.7974 (m-30) cc_final: 0.7278 (p0)
REVERT: B   83 PHE cc_start: 0.8371 (t80) cc_final: 0.7968 (t80)
REVERT: B   88 LEU cc_start: 0.9724 (tt) cc_final: 0.9509 (tt)
REVERT: B   93 GLN cc_start: 0.8748 (pp30) cc_final: 0.8395 (pp30)
REVERT: B  184 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8265 (mm-30)
REVERT: B  405 TYR cc_start: 0.9104 (t80) cc_final: 0.8693 (t80)
REVERT: B  451 MET cc_start: 0.8688 (mmp) cc_final: 0.7947 (mmp)
REVERT: C   83 PHE cc_start: 0.8487 (t80) cc_final: 0.7670 (t80)
REVERT: C   93 GLN cc_start: 0.8783 (pp30) cc_final: 0.8427 (pp30)
REVERT: C  108 MET cc_start: 0.8602 (tpp) cc_final: 0.8200 (tpp)
REVERT: C  171 LEU cc_start: 0.9537 (tp) cc_final: 0.9325 (tp)
REVERT: C  177 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8327 (ttp)
REVERT: C  184 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8398 (mm-30)
REVERT: C  251 MET cc_start: 0.7868 (tmm) cc_final: 0.7525 (tmm)
REVERT: C  336 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8717 (pp)
REVERT: C  405 TYR cc_start: 0.9166 (t80) cc_final: 0.8831 (t80)
REVERT: C  451 MET cc_start: 0.8702 (mmp) cc_final: 0.7954 (mmp)
REVERT: C  476 ASP cc_start: 0.7838 (m-30) cc_final: 0.7246 (p0)
  outliers start: 40
  outliers final: 27
  residues processed: 234
  average time/residue: 0.2342
  time to fit residues: 81.0286
Evaluate side-chains
  215 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0570
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0770
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.101973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.074059 restraints weight = 34995.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.076242 restraints weight = 18243.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.077676 restraints weight = 12019.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9885  Z= 0.126
  Angle     :  0.690  11.661  13428  Z= 0.339
  Chirality :  0.042   0.190   1689
  Planarity :  0.004   0.034   1641
  Dihedral  :  4.057  23.988   1344
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 27.18 %
    Favored  : 69.79 %
  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 (0.24), residues: 1254
  helix:  1.30 (0.16), residues: 975
  sheet: -1.67 (0.80), residues: 48
  loop : -1.93 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 473 
 HIS   0.001   0.000   HIS A 328 
 PHE   0.027   0.001   PHE B 170 
 TYR   0.018   0.001   TYR C 317 
 ARG   0.001   0.000   ARG C  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  708)
  hydrogen bonds       : angle       3.98229 ( 2124)
  covalent geometry    : bond        0.00275 ( 9885)
  covalent geometry    : angle       0.69044 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 214
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8730 (pp30) cc_final: 0.8027 (pp30)
REVERT: A  184 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8216 (mm-30)
REVERT: A  304 MET cc_start: 0.9025 (tmm) cc_final: 0.8542 (tmm)
REVERT: A  336 LEU cc_start: 0.9111 (tt) cc_final: 0.8835 (pp)
REVERT: A  405 TYR cc_start: 0.8878 (t80) cc_final: 0.8430 (t80)
REVERT: A  451 MET cc_start: 0.8789 (mmp) cc_final: 0.8013 (mmp)
REVERT: B   83 PHE cc_start: 0.8037 (t80) cc_final: 0.7647 (t80)
REVERT: B   93 GLN cc_start: 0.8749 (pp30) cc_final: 0.8344 (pp30)
REVERT: B  177 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (ttp)
REVERT: B  184 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: B  405 TYR cc_start: 0.8808 (t80) cc_final: 0.8324 (t80)
REVERT: B  451 MET cc_start: 0.8712 (mmp) cc_final: 0.7929 (mmp)
REVERT: C   83 PHE cc_start: 0.8129 (t80) cc_final: 0.7889 (t80)
REVERT: C   93 GLN cc_start: 0.8790 (pp30) cc_final: 0.8403 (pp30)
REVERT: C   94 MET cc_start: 0.9051 (ttm) cc_final: 0.8824 (ttm)
REVERT: C  108 MET cc_start: 0.8682 (tpp) cc_final: 0.8178 (tpp)
REVERT: C  184 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8407 (mm-30)
REVERT: C  300 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8884 (tttm)
REVERT: C  336 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8723 (pp)
REVERT: C  405 TYR cc_start: 0.9053 (t80) cc_final: 0.8742 (t80)
REVERT: C  451 MET cc_start: 0.8758 (mmp) cc_final: 0.8093 (mmp)
REVERT: C  476 ASP cc_start: 0.7728 (m-30) cc_final: 0.7090 (p0)
  outliers start: 32
  outliers final: 22
  residues processed: 229
  average time/residue: 0.1823
  time to fit residues: 61.6368
Evaluate side-chains
  217 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 71 optimal weight:   30.0000
   chunk 92 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.102221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.075080 restraints weight = 34809.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.077192 restraints weight = 18133.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.078504 restraints weight = 12003.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9885  Z= 0.163
  Angle     :  0.705  10.284  13428  Z= 0.353
  Chirality :  0.043   0.174   1689
  Planarity :  0.004   0.034   1641
  Dihedral  :  4.145  24.124   1344
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 27.65 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.85 (0.23), residues: 1254
  helix:  1.24 (0.16), residues: 984
  sheet: -1.61 (0.80), residues: 48
  loop : -1.86 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 287 
 HIS   0.003   0.001   HIS C 328 
 PHE   0.019   0.001   PHE B  83 
 TYR   0.020   0.001   TYR B 317 
 ARG   0.002   0.000   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  708)
  hydrogen bonds       : angle       4.08334 ( 2124)
  covalent geometry    : bond        0.00371 ( 9885)
  covalent geometry    : angle       0.70528 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 201
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8793 (pp30) cc_final: 0.8066 (pp30)
REVERT: A  184 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8277 (mm-30)
REVERT: A  304 MET cc_start: 0.8998 (tmm) cc_final: 0.8756 (tmm)
REVERT: A  405 TYR cc_start: 0.8949 (t80) cc_final: 0.8505 (t80)
REVERT: A  451 MET cc_start: 0.8738 (mmp) cc_final: 0.7978 (mmp)
REVERT: A  476 ASP cc_start: 0.7850 (m-30) cc_final: 0.7252 (p0)
REVERT: B   83 PHE cc_start: 0.8224 (t80) cc_final: 0.7881 (t80)
REVERT: B   93 GLN cc_start: 0.8765 (pp30) cc_final: 0.8391 (pp30)
REVERT: B  184 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8328 (mm-30)
REVERT: B  336 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8845 (pp)
REVERT: B  405 TYR cc_start: 0.8976 (t80) cc_final: 0.8553 (t80)
REVERT: B  451 MET cc_start: 0.8670 (mmp) cc_final: 0.7939 (mmp)
REVERT: C   83 PHE cc_start: 0.8365 (t80) cc_final: 0.8055 (t80)
REVERT: C   93 GLN cc_start: 0.8837 (pp30) cc_final: 0.8470 (pp30)
REVERT: C  108 MET cc_start: 0.8747 (tpp) cc_final: 0.8294 (tpp)
REVERT: C  184 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8422 (mm-30)
REVERT: C  316 MET cc_start: 0.9281 (mmm) cc_final: 0.9060 (mmm)
REVERT: C  336 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8789 (pp)
REVERT: C  405 TYR cc_start: 0.9159 (t80) cc_final: 0.8829 (t80)
REVERT: C  451 MET cc_start: 0.8781 (mmp) cc_final: 0.7960 (mmp)
REVERT: C  476 ASP cc_start: 0.7713 (m-30) cc_final: 0.7169 (p0)
  outliers start: 35
  outliers final: 28
  residues processed: 220
  average time/residue: 0.1863
  time to fit residues: 60.9048
Evaluate side-chains
  220 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 190
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 84 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 74 optimal weight:    0.2980
   chunk 113 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.100570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.072151 restraints weight = 35774.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.074259 restraints weight = 18721.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.075635 restraints weight = 12510.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9885  Z= 0.135
  Angle     :  0.719  10.425  13428  Z= 0.353
  Chirality :  0.043   0.183   1689
  Planarity :  0.004   0.033   1641
  Dihedral  :  4.152  24.073   1344
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 28.50 %
    Favored  : 68.75 %
  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:  0.79 (0.23), residues: 1254
  helix:  1.22 (0.16), residues: 981
  sheet: -1.61 (0.80), residues: 48
  loop : -1.97 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 346 
 HIS   0.002   0.001   HIS C 328 
 PHE   0.027   0.001   PHE C 170 
 TYR   0.023   0.001   TYR A 288 
 ARG   0.001   0.000   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  708)
  hydrogen bonds       : angle       4.03994 ( 2124)
  covalent geometry    : bond        0.00304 ( 9885)
  covalent geometry    : angle       0.71879 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.6883 (t80) cc_final: 0.6640 (t80)
REVERT: A   93 GLN cc_start: 0.8788 (pp30) cc_final: 0.8078 (pp30)
REVERT: A  184 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: A  304 MET cc_start: 0.9102 (tmm) cc_final: 0.8796 (tmm)
REVERT: A  316 MET cc_start: 0.9270 (ptm) cc_final: 0.9047 (ppp)
REVERT: A  405 TYR cc_start: 0.8863 (t80) cc_final: 0.8446 (t80)
REVERT: A  451 MET cc_start: 0.8853 (mmp) cc_final: 0.8055 (mmp)
REVERT: B   83 PHE cc_start: 0.8129 (t80) cc_final: 0.7819 (t80)
REVERT: B   93 GLN cc_start: 0.8759 (pp30) cc_final: 0.8359 (pp30)
REVERT: B  177 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8489 (ttp)
REVERT: B  184 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: B  336 LEU cc_start: 0.9118 (tt) cc_final: 0.8820 (pp)
REVERT: B  405 TYR cc_start: 0.8900 (t80) cc_final: 0.8527 (t80)
REVERT: B  451 MET cc_start: 0.8763 (mmp) cc_final: 0.8162 (mmp)
REVERT: C   83 PHE cc_start: 0.8127 (t80) cc_final: 0.7922 (t80)
REVERT: C   93 GLN cc_start: 0.8819 (pp30) cc_final: 0.8451 (pp30)
REVERT: C  184 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8413 (mm-30)
REVERT: C  316 MET cc_start: 0.9365 (mmm) cc_final: 0.9136 (mmm)
REVERT: C  336 LEU cc_start: 0.9106 (tt) cc_final: 0.8857 (pp)
REVERT: C  405 TYR cc_start: 0.9030 (t80) cc_final: 0.8721 (t80)
REVERT: C  451 MET cc_start: 0.8843 (mmp) cc_final: 0.8017 (mmp)
REVERT: C  476 ASP cc_start: 0.7673 (m-30) cc_final: 0.7175 (p0)
  outliers start: 29
  outliers final: 26
  residues processed: 216
  average time/residue: 0.1734
  time to fit residues: 56.3669
Evaluate side-chains
  219 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 113 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.097765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.069102 restraints weight = 36689.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.071247 restraints weight = 18865.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.072655 restraints weight = 12379.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9885  Z= 0.167
  Angle     :  0.746  10.157  13428  Z= 0.370
  Chirality :  0.043   0.170   1689
  Planarity :  0.004   0.033   1641
  Dihedral  :  4.256  25.247   1344
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 28.31 %
    Favored  : 68.75 %
  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:  0.70 (0.23), residues: 1254
  helix:  1.14 (0.16), residues: 984
  sheet: -1.54 (0.79), residues: 48
  loop : -1.94 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 287 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.019   0.001   PHE B  83 
 TYR   0.018   0.002   TYR B 317 
 ARG   0.002   0.000   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  708)
  hydrogen bonds       : angle       4.13987 ( 2124)
  covalent geometry    : bond        0.00381 ( 9885)
  covalent geometry    : angle       0.74610 (13428)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 192
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.6895 (t80) cc_final: 0.6664 (t80)
REVERT: A   93 GLN cc_start: 0.8850 (pp30) cc_final: 0.8126 (pp30)
REVERT: A  184 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8393 (mm-30)
REVERT: A  304 MET cc_start: 0.9239 (tmm) cc_final: 0.8910 (tmm)
REVERT: A  405 TYR cc_start: 0.8906 (t80) cc_final: 0.8494 (t80)
REVERT: A  451 MET cc_start: 0.8916 (mmp) cc_final: 0.8133 (mmp)
REVERT: A  476 ASP cc_start: 0.7920 (m-30) cc_final: 0.7263 (p0)
REVERT: B   83 PHE cc_start: 0.8338 (t80) cc_final: 0.7989 (t80)
REVERT: B   93 GLN cc_start: 0.8776 (pp30) cc_final: 0.8335 (pp30)
REVERT: B   94 MET cc_start: 0.8896 (ttm) cc_final: 0.8646 (ttm)
REVERT: B  184 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8449 (mm-30)
REVERT: B  333 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9460 (mp)
REVERT: B  336 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8883 (pp)
REVERT: B  405 TYR cc_start: 0.8940 (t80) cc_final: 0.8581 (t80)
REVERT: B  451 MET cc_start: 0.8858 (mmp) cc_final: 0.8114 (mmp)
REVERT: C   83 PHE cc_start: 0.8321 (t80) cc_final: 0.8071 (t80)
REVERT: C   93 GLN cc_start: 0.8874 (pp30) cc_final: 0.8496 (pp30)
REVERT: C  108 MET cc_start: 0.8787 (tpt) cc_final: 0.8505 (tpp)
REVERT: C  184 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8555 (mm-30)
REVERT: C  316 MET cc_start: 0.9447 (mmm) cc_final: 0.9209 (mmm)
REVERT: C  336 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8906 (pp)
REVERT: C  451 MET cc_start: 0.8923 (mmp) cc_final: 0.8266 (mmp)
REVERT: C  476 ASP cc_start: 0.7813 (m-30) cc_final: 0.7235 (p0)
  outliers start: 31
  outliers final: 27
  residues processed: 207
  average time/residue: 0.1739
  time to fit residues: 54.0291
Evaluate side-chains
  218 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  294 LEU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain C residue  448 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 35 optimal weight:    0.1980
   chunk 84 optimal weight:   10.0000
   chunk 58 optimal weight:    0.0570
   chunk 49 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5500

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.102806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.075324 restraints weight = 34988.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.077507 restraints weight = 17947.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.078941 restraints weight = 11823.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9885  Z= 0.132
  Angle     :  0.736  11.962  13428  Z= 0.359
  Chirality :  0.043   0.183   1689
  Planarity :  0.004   0.031   1641
  Dihedral  :  4.170  25.901   1344
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 28.22 %
    Favored  : 68.75 %
  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:  0.64 (0.23), residues: 1254
  helix:  1.11 (0.16), residues: 981
  sheet: -1.46 (0.80), residues: 48
  loop : -2.04 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C 287 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.026   0.001   PHE A 170 
 TYR   0.025   0.001   TYR B 317 
 ARG   0.002   0.000   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  708)
  hydrogen bonds       : angle       4.05392 ( 2124)
  covalent geometry    : bond        0.00294 ( 9885)
  covalent geometry    : angle       0.73635 (13428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3691.38 seconds
wall clock time: 67 minutes 55.64 seconds (4075.64 seconds total)