Starting phenix.real_space_refine
on Wed Mar  4 03:14:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7npw_12524/03_2026/7npw_12524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7npw_12524/03_2026/7npw_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_12524/03_2026/7npw_12524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7npw_12524/03_2026/7npw_12524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7npw_12524/03_2026/7npw_12524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7npw_12524/03_2026/7npw_12524.cif"
  }
  resolution = 3.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.41, per 1000 atoms: 0.25
  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: 0.87
  Conformation dependent library (CDL) restraints added in 397.9 milliseconds
  

  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: 0.28
  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: 1.45

  Time building geometry restraints manager: 1.17 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             6.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.760
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.910
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (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
 ARG   0.011   0.001   ARG B 388 
 TYR   0.017   0.001   TYR C 405 
 PHE   0.023   0.001   PHE A 373 
 TRP   0.003   0.000   TRP C 346 
 HIS   0.001   0.000   HIS C 328 

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

*********************** 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  : 0.370 
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: 0.0715
  time to fit residues: 28.2669
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  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.100416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.071788 restraints weight = 35444.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.074165 restraints weight = 17573.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.075688 restraints weight = 11301.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.076616 restraints weight = 8689.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.077123 restraints weight = 7487.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9885  Z= 0.166
  Angle     :  0.633   9.991  13428  Z= 0.325
  Chirality :  0.041   0.134   1689
  Planarity :  0.005   0.034   1641
  Dihedral  :  3.940  19.565   1344
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.39 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.24), residues: 1254
  helix:  1.42 (0.16), residues: 978
  sheet: -1.46 (0.82), residues: 48
  loop : -2.35 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 280 
 TYR   0.019   0.002   TYR B  75 
 PHE   0.015   0.002   PHE A 373 
 TRP   0.003   0.001   TRP A 473 
 HIS   0.001   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9885)
  covalent geometry    : angle       0.63312 (13428)
  hydrogen bonds       : bond        0.03753 (  708)
  hydrogen bonds       : angle       4.08016 ( 2124)

*********************** 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
  237 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 209
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8695 (m-10) cc_final: 0.8272 (t80)
REVERT: A  288 TYR cc_start: 0.9125 (t80) cc_final: 0.8824 (t80)
REVERT: A  336 LEU cc_start: 0.8657 (tt) cc_final: 0.8299 (pp)
REVERT: A  451 MET cc_start: 0.8930 (mmp) cc_final: 0.8478 (mmp)
REVERT: A  476 ASP cc_start: 0.7805 (m-30) cc_final: 0.7155 (p0)
REVERT: B   80 TYR cc_start: 0.8648 (m-10) cc_final: 0.8355 (t80)
REVERT: B   88 LEU cc_start: 0.9759 (tt) cc_final: 0.9517 (tt)
REVERT: B  316 MET cc_start: 0.9330 (mmm) cc_final: 0.9107 (mmm)
REVERT: B  451 MET cc_start: 0.8825 (mmp) cc_final: 0.8325 (mmp)
REVERT: C   80 TYR cc_start: 0.8734 (m-10) cc_final: 0.8231 (t80)
REVERT: C   88 LEU cc_start: 0.9764 (tt) cc_final: 0.9518 (tt)
REVERT: C  108 MET cc_start: 0.9023 (mmm) cc_final: 0.8648 (tpp)
REVERT: C  286 MET cc_start: 0.9076 (mmp) cc_final: 0.8742 (tpp)
REVERT: C  307 MET cc_start: 0.6658 (tmm) cc_final: 0.6148 (tmm)
REVERT: C  316 MET cc_start: 0.9222 (mmm) cc_final: 0.8992 (mmm)
REVERT: C  336 LEU cc_start: 0.8596 (tt) cc_final: 0.8324 (pp)
REVERT: C  405 TYR cc_start: 0.9036 (t80) cc_final: 0.8531 (t80)
REVERT: C  451 MET cc_start: 0.8915 (mmp) cc_final: 0.8192 (mmp)
REVERT: C  476 ASP cc_start: 0.7647 (m-30) cc_final: 0.7056 (p0)
  outliers start: 28
  outliers final: 20
  residues processed: 226
  average time/residue: 0.0731
  time to fit residues: 25.2090
Evaluate side-chains
  200 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  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  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 31 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 120 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   chunk 116 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 25 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    2.2986

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.098547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.070568 restraints weight = 35313.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.072580 restraints weight = 19204.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.073887 restraints weight = 13008.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.074581 restraints weight = 10285.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.075067 restraints weight = 9102.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9885  Z= 0.193
  Angle     :  0.651   9.854  13428  Z= 0.336
  Chirality :  0.041   0.147   1689
  Planarity :  0.004   0.037   1641
  Dihedral  :  4.010  18.811   1344
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 18.75 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.23), residues: 1254
  helix:  1.25 (0.16), residues: 984
  sheet: -1.41 (0.81), residues: 48
  loop : -2.02 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 280 
 TYR   0.016   0.002   TYR B  75 
 PHE   0.018   0.002   PHE B  83 
 TRP   0.003   0.001   TRP B 287 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9885)
  covalent geometry    : angle       0.65084 (13428)
  hydrogen bonds       : bond        0.03797 (  708)
  hydrogen bonds       : angle       4.13753 ( 2124)

*********************** 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
  229 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8657 (m-10) cc_final: 0.8388 (t80)
REVERT: A  336 LEU cc_start: 0.8914 (tt) cc_final: 0.8682 (pp)
REVERT: A  451 MET cc_start: 0.8740 (mmp) cc_final: 0.8291 (mmp)
REVERT: A  476 ASP cc_start: 0.7942 (m-30) cc_final: 0.7217 (p0)
REVERT: B  242 ASN cc_start: 0.8957 (t0) cc_final: 0.8680 (t0)
REVERT: B  303 GLU cc_start: 0.8801 (pp20) cc_final: 0.8596 (pp20)
REVERT: B  451 MET cc_start: 0.8692 (mmp) cc_final: 0.8174 (mmp)
REVERT: C   80 TYR cc_start: 0.8570 (m-10) cc_final: 0.8360 (t80)
REVERT: C   88 LEU cc_start: 0.9786 (tt) cc_final: 0.9522 (tt)
REVERT: C  242 ASN cc_start: 0.8833 (t0) cc_final: 0.8566 (t0)
REVERT: C  286 MET cc_start: 0.9016 (mmp) cc_final: 0.8759 (tpt)
REVERT: C  316 MET cc_start: 0.9326 (mmm) cc_final: 0.9064 (mmm)
REVERT: C  336 LEU cc_start: 0.8826 (tt) cc_final: 0.8562 (pp)
REVERT: C  405 TYR cc_start: 0.9186 (t80) cc_final: 0.8806 (t80)
REVERT: C  451 MET cc_start: 0.8763 (mmp) cc_final: 0.8065 (mmp)
REVERT: C  476 ASP cc_start: 0.7866 (m-30) cc_final: 0.7183 (p0)
  outliers start: 42
  outliers final: 29
  residues processed: 215
  average time/residue: 0.0716
  time to fit residues: 23.4036
Evaluate side-chains
  197 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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  252 CYS
Chi-restraints excluded: chain A residue  282 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   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  256 VAL
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  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 123 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 117 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 119 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.101250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.073047 restraints weight = 35534.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.075210 restraints weight = 18991.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076629 restraints weight = 12575.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.077170 restraints weight = 9761.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.077892 restraints weight = 8661.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3193

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= 0.122
  Angle     :  0.619  10.650  13428  Z= 0.312
  Chirality :  0.041   0.173   1689
  Planarity :  0.004   0.035   1641
  Dihedral  :  3.914  19.498   1344
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.21 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.23), residues: 1254
  helix:  1.41 (0.16), residues: 984
  sheet: -1.55 (0.80), residues: 48
  loop : -2.00 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 280 
 TYR   0.026   0.002   TYR B 288 
 PHE   0.018   0.001   PHE B  83 
 TRP   0.002   0.000   TRP C 346 
 HIS   0.001   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9885)
  covalent geometry    : angle       0.61942 (13428)
  hydrogen bonds       : bond        0.03445 (  708)
  hydrogen bonds       : angle       3.94440 ( 2124)

*********************** 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
  246 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 209
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8653 (m-10) cc_final: 0.8334 (t80)
REVERT: A  242 ASN cc_start: 0.8866 (t0) cc_final: 0.8638 (t0)
REVERT: A  336 LEU cc_start: 0.8967 (tt) cc_final: 0.8688 (pp)
REVERT: A  405 TYR cc_start: 0.9011 (t80) cc_final: 0.8601 (t80)
REVERT: A  451 MET cc_start: 0.8757 (mmp) cc_final: 0.8220 (mmp)
REVERT: A  476 ASP cc_start: 0.7892 (m-30) cc_final: 0.7252 (p0)
REVERT: B  242 ASN cc_start: 0.8865 (t0) cc_final: 0.8647 (t0)
REVERT: B  451 MET cc_start: 0.8713 (mmp) cc_final: 0.8114 (mmp)
REVERT: C   80 TYR cc_start: 0.8702 (m-10) cc_final: 0.8357 (t80)
REVERT: C   83 PHE cc_start: 0.8381 (t80) cc_final: 0.8066 (t80)
REVERT: C  177 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8224 (ttp)
REVERT: C  184 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8266 (mm-30)
REVERT: C  242 ASN cc_start: 0.8757 (t0) cc_final: 0.8556 (t0)
REVERT: C  316 MET cc_start: 0.9362 (mmm) cc_final: 0.9122 (mmm)
REVERT: C  336 LEU cc_start: 0.8920 (tt) cc_final: 0.8595 (pp)
REVERT: C  405 TYR cc_start: 0.9099 (t80) cc_final: 0.8657 (t80)
REVERT: C  451 MET cc_start: 0.8808 (mmp) cc_final: 0.8031 (mmp)
REVERT: C  476 ASP cc_start: 0.7808 (m-30) cc_final: 0.7199 (p0)
  outliers start: 37
  outliers final: 24
  residues processed: 227
  average time/residue: 0.0792
  time to fit residues: 27.1978
Evaluate side-chains
  209 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  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  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  281 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 124 optimal weight:   10.0000
   chunk 63 optimal weight:    0.5980
   chunk 41 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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**
B 425 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.100326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.072338 restraints weight = 35197.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.074499 restraints weight = 18435.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.075892 restraints weight = 12294.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076567 restraints weight = 9580.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.076789 restraints weight = 8461.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3457

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= 0.144
  Angle     :  0.641  10.467  13428  Z= 0.322
  Chirality :  0.041   0.166   1689
  Planarity :  0.004   0.037   1641
  Dihedral  :  3.940  19.622   1344
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.77 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.23), residues: 1254
  helix:  1.42 (0.16), residues: 978
  sheet: -1.56 (0.80), residues: 48
  loop : -1.93 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 280 
 TYR   0.022   0.002   TYR B 288 
 PHE   0.020   0.001   PHE C 170 
 TRP   0.002   0.000   TRP B 346 
 HIS   0.002   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9885)
  covalent geometry    : angle       0.64072 (13428)
  hydrogen bonds       : bond        0.03519 (  708)
  hydrogen bonds       : angle       3.99297 ( 2124)

*********************** 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
  246 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 202
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8669 (m-10) cc_final: 0.8431 (t80)
REVERT: A   93 GLN cc_start: 0.8616 (pp30) cc_final: 0.7936 (pp30)
REVERT: A  242 ASN cc_start: 0.8859 (t0) cc_final: 0.8604 (t0)
REVERT: A  336 LEU cc_start: 0.9016 (tt) cc_final: 0.8728 (pp)
REVERT: A  451 MET cc_start: 0.8804 (mmp) cc_final: 0.8249 (mmp)
REVERT: A  476 ASP cc_start: 0.7845 (m-30) cc_final: 0.7192 (p0)
REVERT: B   83 PHE cc_start: 0.8501 (t80) cc_final: 0.8107 (t80)
REVERT: B   93 GLN cc_start: 0.8636 (pp30) cc_final: 0.8292 (pp30)
REVERT: B   94 MET cc_start: 0.8956 (ttm) cc_final: 0.8724 (ttm)
REVERT: B  405 TYR cc_start: 0.9072 (t80) cc_final: 0.8661 (t80)
REVERT: B  451 MET cc_start: 0.8773 (mmp) cc_final: 0.8026 (mmp)
REVERT: C   80 TYR cc_start: 0.8633 (m-10) cc_final: 0.8426 (t80)
REVERT: C   83 PHE cc_start: 0.8494 (t80) cc_final: 0.8119 (t80)
REVERT: C   93 GLN cc_start: 0.8684 (pp30) cc_final: 0.8359 (pp30)
REVERT: C  108 MET cc_start: 0.8512 (tpp) cc_final: 0.8142 (tpp)
REVERT: C  184 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: C  251 MET cc_start: 0.7868 (tmm) cc_final: 0.7606 (tmm)
REVERT: C  316 MET cc_start: 0.9385 (mmm) cc_final: 0.9169 (mmm)
REVERT: C  336 LEU cc_start: 0.8975 (tt) cc_final: 0.8606 (pp)
REVERT: C  405 TYR cc_start: 0.9104 (t80) cc_final: 0.8689 (t80)
REVERT: C  451 MET cc_start: 0.8819 (mmp) cc_final: 0.8190 (mmp)
REVERT: C  476 ASP cc_start: 0.7798 (m-30) cc_final: 0.7200 (p0)
  outliers start: 44
  outliers final: 27
  residues processed: 228
  average time/residue: 0.0723
  time to fit residues: 24.7717
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  : 0.356 
-------------------------------------------------------------------------------
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  126 TYR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 VAL
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  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  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 64 optimal weight:    0.8980
   chunk 113 optimal weight:   30.0000
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 102 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0000
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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**
** C 425 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 = 0.3857 r_free = 0.3857 target = 0.102014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.074038 restraints weight = 34924.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.076181 restraints weight = 18195.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.077593 restraints weight = 12122.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.078347 restraints weight = 9451.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.078853 restraints weight = 8301.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9885  Z= 0.122
  Angle     :  0.661  11.995  13428  Z= 0.323
  Chirality :  0.042   0.182   1689
  Planarity :  0.004   0.033   1641
  Dihedral  :  3.971  22.868   1344
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 24.43 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.24), residues: 1254
  helix:  1.44 (0.16), residues: 978
  sheet: -1.59 (0.80), residues: 48
  loop : -2.01 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 479 
 TYR   0.025   0.001   TYR C 288 
 PHE   0.020   0.001   PHE B 170 
 TRP   0.003   0.000   TRP C 346 
 HIS   0.001   0.000   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9885)
  covalent geometry    : angle       0.66076 (13428)
  hydrogen bonds       : bond        0.03413 (  708)
  hydrogen bonds       : angle       3.94683 ( 2124)

*********************** 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
  255 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 218
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8657 (m-10) cc_final: 0.8359 (t80)
REVERT: A   83 PHE cc_start: 0.8387 (t80) cc_final: 0.7737 (t80)
REVERT: A   93 GLN cc_start: 0.8664 (pp30) cc_final: 0.7963 (pp30)
REVERT: A  242 ASN cc_start: 0.8789 (t0) cc_final: 0.8539 (t0)
REVERT: A  303 GLU cc_start: 0.8781 (pp20) cc_final: 0.8576 (pp20)
REVERT: A  336 LEU cc_start: 0.9000 (tt) cc_final: 0.8723 (pp)
REVERT: A  405 TYR cc_start: 0.8868 (t80) cc_final: 0.8374 (t80)
REVERT: A  451 MET cc_start: 0.8770 (mmp) cc_final: 0.7914 (mmp)
REVERT: B   83 PHE cc_start: 0.8319 (t80) cc_final: 0.7906 (t80)
REVERT: B   93 GLN cc_start: 0.8634 (pp30) cc_final: 0.8286 (pp30)
REVERT: B  177 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8420 (ttp)
REVERT: B  288 TYR cc_start: 0.8953 (t80) cc_final: 0.8606 (t80)
REVERT: B  405 TYR cc_start: 0.8993 (t80) cc_final: 0.8548 (t80)
REVERT: B  451 MET cc_start: 0.8691 (mmp) cc_final: 0.7881 (mmp)
REVERT: B  472 ASP cc_start: 0.8843 (p0) cc_final: 0.8533 (p0)
REVERT: C   80 TYR cc_start: 0.8617 (m-10) cc_final: 0.8402 (t80)
REVERT: C   83 PHE cc_start: 0.8247 (t80) cc_final: 0.7650 (t80)
REVERT: C   93 GLN cc_start: 0.8727 (pp30) cc_final: 0.8365 (pp30)
REVERT: C  108 MET cc_start: 0.8413 (tpp) cc_final: 0.8073 (tpp)
REVERT: C  316 MET cc_start: 0.9375 (mmm) cc_final: 0.9173 (mmm)
REVERT: C  336 LEU cc_start: 0.8985 (tt) cc_final: 0.8683 (pp)
REVERT: C  405 TYR cc_start: 0.9045 (t80) cc_final: 0.8630 (t80)
REVERT: C  451 MET cc_start: 0.8718 (mmp) cc_final: 0.7964 (mmp)
REVERT: C  476 ASP cc_start: 0.7745 (m-30) cc_final: 0.7090 (p0)
  outliers start: 37
  outliers final: 27
  residues processed: 235
  average time/residue: 0.0709
  time to fit residues: 25.2550
Evaluate side-chains
  221 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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 A residue  464 ASP
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 62 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0170
   chunk 63 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0270
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.102844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.075117 restraints weight = 34629.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.077340 restraints weight = 18197.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.078789 restraints weight = 12083.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.079618 restraints weight = 9388.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.080001 restraints weight = 8117.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9885  Z= 0.124
  Angle     :  0.686  11.413  13428  Z= 0.334
  Chirality :  0.042   0.190   1689
  Planarity :  0.004   0.032   1641
  Dihedral  :  3.918  20.332   1344
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.23 %
    Favored  : 70.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.24), residues: 1254
  helix:  1.43 (0.17), residues: 975
  sheet: -1.63 (0.80), residues: 48
  loop : -1.99 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 479 
 TYR   0.019   0.001   TYR A  75 
 PHE   0.023   0.001   PHE A  83 
 TRP   0.002   0.000   TRP C 346 
 HIS   0.002   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9885)
  covalent geometry    : angle       0.68625 (13428)
  hydrogen bonds       : bond        0.03429 (  708)
  hydrogen bonds       : angle       3.96522 ( 2124)

*********************** 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
  247 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 209
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.8601 (m-10) cc_final: 0.8350 (t80)
REVERT: A   93 GLN cc_start: 0.8697 (pp30) cc_final: 0.8013 (pp30)
REVERT: A  242 ASN cc_start: 0.8773 (t0) cc_final: 0.8510 (t0)
REVERT: A  303 GLU cc_start: 0.8810 (pp20) cc_final: 0.8594 (pp20)
REVERT: A  336 LEU cc_start: 0.8994 (tt) cc_final: 0.8751 (pp)
REVERT: A  405 TYR cc_start: 0.8692 (t80) cc_final: 0.8330 (t80)
REVERT: A  451 MET cc_start: 0.8723 (mmp) cc_final: 0.7862 (mmp)
REVERT: B   83 PHE cc_start: 0.8162 (t80) cc_final: 0.7846 (t80)
REVERT: B   93 GLN cc_start: 0.8669 (pp30) cc_final: 0.8306 (pp30)
REVERT: B  177 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (ttp)
REVERT: B  405 TYR cc_start: 0.8791 (t80) cc_final: 0.8307 (t80)
REVERT: B  451 MET cc_start: 0.8590 (mmp) cc_final: 0.7797 (mmp)
REVERT: B  476 ASP cc_start: 0.7801 (m-30) cc_final: 0.7392 (t0)
REVERT: C   93 GLN cc_start: 0.8708 (pp30) cc_final: 0.8334 (pp30)
REVERT: C  108 MET cc_start: 0.8412 (tpp) cc_final: 0.8096 (tpp)
REVERT: C  171 LEU cc_start: 0.9413 (tp) cc_final: 0.9135 (tp)
REVERT: C  177 MET cc_start: 0.8575 (ttp) cc_final: 0.8255 (ttm)
REVERT: C  316 MET cc_start: 0.9380 (mmm) cc_final: 0.9172 (mmm)
REVERT: C  336 LEU cc_start: 0.8999 (tt) cc_final: 0.8716 (pp)
REVERT: C  405 TYR cc_start: 0.8988 (t80) cc_final: 0.8498 (t80)
REVERT: C  451 MET cc_start: 0.8750 (mmp) cc_final: 0.7919 (mmp)
  outliers start: 38
  outliers final: 27
  residues processed: 227
  average time/residue: 0.0710
  time to fit residues: 24.5532
Evaluate side-chains
  225 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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   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  140 ILE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 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  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  448 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 105 optimal weight:    0.8980
   chunk 92 optimal weight:    0.1980
   chunk 58 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 415 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 = 0.3874 r_free = 0.3874 target = 0.102930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075330 restraints weight = 35100.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.077436 restraints weight = 18622.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.078794 restraints weight = 12504.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.079513 restraints weight = 9839.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.079985 restraints weight = 8678.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9885  Z= 0.128
  Angle     :  0.687  10.444  13428  Z= 0.339
  Chirality :  0.042   0.187   1689
  Planarity :  0.004   0.031   1641
  Dihedral  :  4.003  25.458   1344
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 27.18 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.24), residues: 1254
  helix:  1.39 (0.16), residues: 975
  sheet: -1.65 (0.80), residues: 48
  loop : -1.95 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 477 
 TYR   0.019   0.001   TYR C  75 
 PHE   0.025   0.001   PHE A  83 
 TRP   0.005   0.000   TRP B 473 
 HIS   0.001   0.000   HIS C 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9885)
  covalent geometry    : angle       0.68678 (13428)
  hydrogen bonds       : bond        0.03447 (  708)
  hydrogen bonds       : angle       3.99808 ( 2124)

*********************** 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
  245 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8646 (pp30) cc_final: 0.7962 (pp30)
REVERT: A  303 GLU cc_start: 0.8717 (pp20) cc_final: 0.8471 (pp20)
REVERT: A  336 LEU cc_start: 0.8996 (tt) cc_final: 0.8755 (pp)
REVERT: A  405 TYR cc_start: 0.8756 (t80) cc_final: 0.8355 (t80)
REVERT: A  451 MET cc_start: 0.8657 (mmp) cc_final: 0.7821 (mmp)
REVERT: B   83 PHE cc_start: 0.8195 (t80) cc_final: 0.7865 (t80)
REVERT: B  177 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (ttp)
REVERT: B  405 TYR cc_start: 0.8896 (t80) cc_final: 0.8404 (t80)
REVERT: B  451 MET cc_start: 0.8499 (mmp) cc_final: 0.7765 (mmp)
REVERT: C   93 GLN cc_start: 0.8699 (pp30) cc_final: 0.8341 (pp30)
REVERT: C  108 MET cc_start: 0.8350 (tpp) cc_final: 0.8081 (tpp)
REVERT: C  177 MET cc_start: 0.8522 (ttp) cc_final: 0.8224 (ttm)
REVERT: C  336 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8760 (pp)
REVERT: C  405 TYR cc_start: 0.9020 (t80) cc_final: 0.8550 (t80)
REVERT: C  451 MET cc_start: 0.8630 (mmp) cc_final: 0.7846 (mmp)
  outliers start: 35
  outliers final: 27
  residues processed: 227
  average time/residue: 0.0707
  time to fit residues: 24.3888
Evaluate side-chains
  224 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 195
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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   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  140 ILE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 121 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 102 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0870
   chunk 12 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.6960

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.102902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.075515 restraints weight = 34638.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.077634 restraints weight = 18619.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.079001 restraints weight = 12522.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.079801 restraints weight = 9818.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.080182 restraints weight = 8534.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3910

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= 0.129
  Angle     :  0.709  12.008  13428  Z= 0.349
  Chirality :  0.042   0.200   1689
  Planarity :  0.004   0.031   1641
  Dihedral  :  3.979  24.820   1344
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 27.65 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.24), residues: 1254
  helix:  1.34 (0.16), residues: 981
  sheet: -1.67 (0.80), residues: 48
  loop : -1.90 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 479 
 TYR   0.024   0.001   TYR C 317 
 PHE   0.021   0.001   PHE C 170 
 TRP   0.002   0.000   TRP C 346 
 HIS   0.001   0.000   HIS C 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9885)
  covalent geometry    : angle       0.70888 (13428)
  hydrogen bonds       : bond        0.03483 (  708)
  hydrogen bonds       : angle       4.01456 ( 2124)

*********************** 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
  241 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8690 (pp30) cc_final: 0.8004 (pp30)
REVERT: A  303 GLU cc_start: 0.8722 (pp20) cc_final: 0.8497 (pp20)
REVERT: A  336 LEU cc_start: 0.9004 (tt) cc_final: 0.8755 (pp)
REVERT: A  405 TYR cc_start: 0.8793 (t80) cc_final: 0.8341 (t80)
REVERT: A  451 MET cc_start: 0.8683 (mmp) cc_final: 0.7833 (mmp)
REVERT: B   83 PHE cc_start: 0.8159 (t80) cc_final: 0.7766 (t80)
REVERT: B  177 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (ttp)
REVERT: B  251 MET cc_start: 0.7999 (tmm) cc_final: 0.7766 (tmm)
REVERT: B  405 TYR cc_start: 0.8900 (t80) cc_final: 0.8455 (t80)
REVERT: B  451 MET cc_start: 0.8559 (mmp) cc_final: 0.7834 (mmp)
REVERT: B  472 ASP cc_start: 0.8771 (p0) cc_final: 0.8365 (m-30)
REVERT: C   93 GLN cc_start: 0.8772 (pp30) cc_final: 0.8417 (pp30)
REVERT: C  108 MET cc_start: 0.8413 (tpp) cc_final: 0.8119 (tpp)
REVERT: C  170 PHE cc_start: 0.9109 (t80) cc_final: 0.8861 (t80)
REVERT: C  177 MET cc_start: 0.8590 (ttp) cc_final: 0.8244 (ttm)
REVERT: C  336 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8745 (pp)
REVERT: C  405 TYR cc_start: 0.8994 (t80) cc_final: 0.8534 (t80)
REVERT: C  451 MET cc_start: 0.8706 (mmp) cc_final: 0.7881 (mmp)
  outliers start: 37
  outliers final: 28
  residues processed: 225
  average time/residue: 0.0690
  time to fit residues: 23.8853
Evaluate side-chains
  225 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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   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  140 ILE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  232 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  333 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 121 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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**
** C 425 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 = 0.3847 r_free = 0.3847 target = 0.101519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.073964 restraints weight = 34918.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.076033 restraints weight = 18922.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.077368 restraints weight = 12630.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078151 restraints weight = 9912.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.078358 restraints weight = 8642.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9885  Z= 0.146
  Angle     :  0.717  11.414  13428  Z= 0.359
  Chirality :  0.042   0.180   1689
  Planarity :  0.004   0.032   1641
  Dihedral  :  4.053  24.093   1344
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.22 %
    Favored  : 68.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.24), residues: 1254
  helix:  1.34 (0.16), residues: 975
  sheet: -1.59 (0.80), residues: 48
  loop : -1.69 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 479 
 TYR   0.021   0.001   TYR B 288 
 PHE   0.027   0.001   PHE A  83 
 TRP   0.002   0.000   TRP B 346 
 HIS   0.003   0.001   HIS C 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9885)
  covalent geometry    : angle       0.71658 (13428)
  hydrogen bonds       : bond        0.03728 (  708)
  hydrogen bonds       : angle       4.09673 ( 2124)

********************** 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
  228 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TYR cc_start: 0.6889 (t80) cc_final: 0.6579 (t80)
REVERT: A   93 GLN cc_start: 0.8729 (pp30) cc_final: 0.8038 (pp30)
REVERT: A  303 GLU cc_start: 0.8838 (pp20) cc_final: 0.8627 (pp20)
REVERT: A  336 LEU cc_start: 0.9059 (tt) cc_final: 0.8785 (pp)
REVERT: A  405 TYR cc_start: 0.8889 (t80) cc_final: 0.8419 (t80)
REVERT: A  451 MET cc_start: 0.8743 (mmp) cc_final: 0.7908 (mmp)
REVERT: B   83 PHE cc_start: 0.8207 (t80) cc_final: 0.7925 (t80)
REVERT: B   93 GLN cc_start: 0.8696 (pp30) cc_final: 0.8392 (pp30)
REVERT: B  177 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8445 (ttp)
REVERT: B  251 MET cc_start: 0.7995 (tmm) cc_final: 0.7754 (tmm)
REVERT: B  336 LEU cc_start: 0.9109 (tt) cc_final: 0.8820 (pp)
REVERT: B  405 TYR cc_start: 0.8905 (t80) cc_final: 0.8503 (t80)
REVERT: B  451 MET cc_start: 0.8600 (mmp) cc_final: 0.7891 (mmp)
REVERT: C   93 GLN cc_start: 0.8790 (pp30) cc_final: 0.8421 (pp30)
REVERT: C  108 MET cc_start: 0.8490 (tpp) cc_final: 0.8199 (tpp)
REVERT: C  177 MET cc_start: 0.8598 (ttp) cc_final: 0.8250 (ttm)
REVERT: C  303 GLU cc_start: 0.8696 (pp20) cc_final: 0.8300 (pp20)
REVERT: C  336 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8780 (pp)
REVERT: C  405 TYR cc_start: 0.9058 (t80) cc_final: 0.8619 (t80)
REVERT: C  451 MET cc_start: 0.8732 (mmp) cc_final: 0.7921 (mmp)
  outliers start: 34
  outliers final: 29
  residues processed: 213
  average time/residue: 0.0652
  time to fit residues: 21.5227
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  : 0.333 
-------------------------------------------------------------------------------
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  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   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  140 ILE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  232 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  333 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  174 ILE
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 73 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 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 = 0.3744 r_free = 0.3744 target = 0.096702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.068437 restraints weight = 36396.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.070448 restraints weight = 18920.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.071770 restraints weight = 12588.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.072534 restraints weight = 9870.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072758 restraints weight = 8629.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4577

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= 0.192
  Angle     :  0.738  11.379  13428  Z= 0.377
  Chirality :  0.043   0.158   1689
  Planarity :  0.004   0.033   1641
  Dihedral  :  4.266  24.574   1344
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.31 %
    Favored  : 68.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.23), residues: 1254
  helix:  1.15 (0.16), residues: 978
  sheet: -1.41 (0.80), residues: 48
  loop : -1.47 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 280 
 TYR   0.026   0.002   TYR B 288 
 PHE   0.027   0.002   PHE A  83 
 TRP   0.004   0.001   TRP A 287 
 HIS   0.003   0.001   HIS C 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 9885)
  covalent geometry    : angle       0.73827 (13428)
  hydrogen bonds       : bond        0.04034 (  708)
  hydrogen bonds       : angle       4.26174 ( 2124)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1722.12 seconds
wall clock time: 30 minutes 23.93 seconds (1823.93 seconds total)