Starting phenix.real_space_refine
on Wed Jul 30 02:28:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jfy_36219/07_2025/8jfy_36219.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Ca     12      9.91       5
     Fe      2      7.16       5
     Zn      2      6.06       5
     P       2      5.49       5
     S      66      5.16       5
     C    7456      2.51       5
     N    2058      2.21       5
     O    2272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11870
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1172
          Classifications: {'peptide': 149}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 146}
    Chain: "C"
      Number of atoms: 4750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4750
          Classifications: {'peptide': 587}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 564}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 9
          Unusual residues: {' CA': 2, ' FE': 1, ' ZN': 1, 'PO4': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 10.31, per 1000 atoms: 0.87
  Number of scatterers: 11870
  At special positions: 0
  Unit cell: (84.645, 170.145, 106.875, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      2     29.99
     Fe      2     26.01
     Ca     12     19.99
     S      66     16.00
     P       2     15.00
     O    2272      8.00
     N    2058      7.00
     C    7456      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.90
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 701 "
        pdb="ZN    ZN C 701 " - pdb=" NE2 HIS C 360 "
        pdb="ZN    ZN C 701 " - pdb=" NE2 HIS C 271 "
      pdb="  ZN D 701 "
        pdb="ZN    ZN D 701 " - pdb=" NE2 HIS D 360 "
        pdb="ZN    ZN D 701 " - pdb=" NE2 HIS D 271 "


  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2776

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 10 sheets defined
      57.9% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 5
      removed outlier: 4.046A  pdb=" N   GLN A   4 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 21
      removed outlier: 4.081A  pdb=" N   GLU A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLU A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE A  20 " --> pdb=" O   ALA A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 45 through 56
      removed outlier: 4.820A  pdb=" N   ASP A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A  54 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 79
      removed outlier: 3.557A  pdb=" N   ASP A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 94
      removed outlier: 4.083A  pdb=" N   GLU A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 114
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 138 through 148
    Processing helix  chain 'D' and resid 2 through 29
      removed outlier: 3.754A  pdb=" N   ILE D   6 " --> pdb=" O   ASP D   2 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET D  25 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 44
      removed outlier: 3.865A  pdb=" N   ASN D  36 " --> pdb=" O   GLN D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 52
      removed outlier: 3.979A  pdb=" N   LYS D  50 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE D  51 " --> pdb=" O   GLU D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 114
      removed outlier: 3.745A  pdb=" N   LYS D 114 " --> pdb=" O   ASP D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 139
      removed outlier: 3.897A  pdb=" N   GLN D 138 " --> pdb=" O   LYS D 134 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU D 139 " --> pdb=" O   SER D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 174
    Processing helix  chain 'D' and resid 194 through 209
    Processing helix  chain 'D' and resid 222 through 230
    Processing helix  chain 'D' and resid 230 through 239
    Processing helix  chain 'D' and resid 242 through 257
      removed outlier: 3.577A  pdb=" N   GLU D 252 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 279 through 284
    Processing helix  chain 'D' and resid 306 through 319
      removed outlier: 3.655A  pdb=" N   GLN D 312 " --> pdb=" O   THR D 308 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE D 313 " --> pdb=" O   GLU D 309 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 352
    Processing helix  chain 'D' and resid 413 through 418
      removed outlier: 3.863A  pdb=" N   LYS D 416 " --> pdb=" O   SER D 413 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU D 418 " --> pdb=" O   THR D 415 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 427 through 439
      removed outlier: 3.531A  pdb=" N   ALA D 431 " --> pdb=" O   VAL D 427 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LYS D 433 " --> pdb=" O   SER D 429 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 442 through 454
    Processing helix  chain 'D' and resid 463 through 474
    Processing helix  chain 'D' and resid 479 through 488
      removed outlier: 4.623A  pdb=" N   ASP D 485 " --> pdb=" O   ARG D 481 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   LYS D 486 " --> pdb=" O   LEU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 507
      removed outlier: 3.511A  pdb=" N   LEU D 505 " --> pdb=" O   THR D 501 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 507 through 513
      removed outlier: 4.011A  pdb=" N   LEU D 511 " --> pdb=" O   THR D 507 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 519 through 526
      removed outlier: 3.610A  pdb=" N   ALA D 523 " --> pdb=" O   SER D 519 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA D 526 " --> pdb=" O   ASP D 522 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 530 through 539
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.633A  pdb=" N   LEU D 557 " --> pdb=" O   THR D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 567 through 579
      removed outlier: 4.001A  pdb=" N   ASP D 579 " --> pdb=" O   CYS D 575 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 587 through 605
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 4.045A  pdb=" N   GLN B   4 " --> pdb=" O   MET B   1 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 21
      removed outlier: 4.081A  pdb=" N   GLU B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLU B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE B  20 " --> pdb=" O   ALA B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 40
    Processing helix  chain 'B' and resid 45 through 56
      removed outlier: 4.820A  pdb=" N   ASP B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN B  54 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 79
      removed outlier: 3.557A  pdb=" N   ASP B  79 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 94
      removed outlier: 4.084A  pdb=" N   GLU B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B  86 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 118 through 130
    Processing helix  chain 'B' and resid 138 through 148
    Processing helix  chain 'C' and resid 2 through 29
      removed outlier: 3.754A  pdb=" N   ILE C   6 " --> pdb=" O   ASP C   2 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   MET C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 44
      removed outlier: 3.865A  pdb=" N   ASN C  36 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 52
      removed outlier: 3.978A  pdb=" N   LYS C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE C  51 " --> pdb=" O   GLU C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 114
      removed outlier: 3.745A  pdb=" N   LYS C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 139
      removed outlier: 3.897A  pdb=" N   GLN C 138 " --> pdb=" O   LYS C 134 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU C 139 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 174
    Processing helix  chain 'C' and resid 194 through 209
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 230 through 239
    Processing helix  chain 'C' and resid 242 through 257
      removed outlier: 3.577A  pdb=" N   GLU C 252 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 284
    Processing helix  chain 'C' and resid 306 through 319
      removed outlier: 3.655A  pdb=" N   GLN C 312 " --> pdb=" O   THR C 308 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE C 313 " --> pdb=" O   GLU C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 352
    Processing helix  chain 'C' and resid 413 through 418
      removed outlier: 3.863A  pdb=" N   LYS C 416 " --> pdb=" O   SER C 413 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU C 418 " --> pdb=" O   THR C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 439
      removed outlier: 3.531A  pdb=" N   ALA C 431 " --> pdb=" O   VAL C 427 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LYS C 433 " --> pdb=" O   SER C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 454
    Processing helix  chain 'C' and resid 463 through 474
    Processing helix  chain 'C' and resid 479 through 488
      removed outlier: 4.623A  pdb=" N   ASP C 485 " --> pdb=" O   ARG C 481 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   LYS C 486 " --> pdb=" O   LEU C 482 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 498 through 507
      removed outlier: 3.512A  pdb=" N   LEU C 505 " --> pdb=" O   THR C 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 513
      removed outlier: 4.011A  pdb=" N   LEU C 511 " --> pdb=" O   THR C 507 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 519 through 526
      removed outlier: 3.610A  pdb=" N   ALA C 523 " --> pdb=" O   SER C 519 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA C 526 " --> pdb=" O   ASP C 522 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 530 through 539
    Processing helix  chain 'C' and resid 547 through 559
      removed outlier: 3.634A  pdb=" N   LEU C 557 " --> pdb=" O   THR C 553 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 567 through 579
      removed outlier: 4.001A  pdb=" N   ASP C 579 " --> pdb=" O   CYS C 575 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 587 through 605
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28
    Processing sheet with id=AA2, first strand: chain 'D' and resid 142 through 145
      removed outlier: 6.497A  pdb=" N   LEU D 268 " --> pdb=" O   ILE D 357 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 215
    Processing sheet with id=AA4, first strand: chain 'D' and resid 320 through 321
    Processing sheet with id=AA5, first strand: chain 'D' and resid 460 through 462
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 28
    Processing sheet with id=AA7, first strand: chain 'C' and resid 142 through 145
      removed outlier: 6.496A  pdb=" N   LEU C 268 " --> pdb=" O   ILE C 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 213 through 215
    Processing sheet with id=AA9, first strand: chain 'C' and resid 320 through 321
    Processing sheet with id=AB1, first strand: chain 'C' and resid 460 through 462

    592 hydrogen bonds defined for protein.
    1734 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: 3.57

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2271
        1.33 -     1.45: 2941
        1.45 -     1.57: 6742
        1.57 -     1.69: 0
        1.69 -     1.82: 120
  Bond restraints: 12074
  Sorted by residual:
  bond pdb=" CA  HIS C 360 "
       pdb=" C   HIS C 360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.051 1.34e-02 5.57e+03 1.43e+01
  bond pdb=" CA  SER D 359 "
       pdb=" C   SER D 359 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 1.26e-02 6.30e+03 1.40e+01
  bond pdb=" CA  SER C 359 "
       pdb=" C   SER C 359 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 1.26e-02 6.30e+03 1.40e+01
  bond pdb=" CA  HIS D 360 "
       pdb=" C   HIS D 360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.34e-02 5.57e+03 1.39e+01
  bond pdb=" C   VAL C 356 "
       pdb=" O   VAL C 356 "
    ideal  model  delta    sigma   weight residual
    1.236  1.204  0.032 1.00e-02 1.00e+04 1.01e+01
  ... (remaining 12069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 15899
        1.62 -     3.25: 310
        3.25 -     4.87: 52
        4.87 -     6.49: 11
        6.49 -     8.11: 14
  Bond angle restraints: 16286
  Sorted by residual:
  angle pdb=" C   GLU D 361 "
        pdb=" N   CYS D 362 "
        pdb=" CA  CYS D 362 "
      ideal   model   delta    sigma   weight residual
     120.87  128.98   -8.11 1.42e+00 4.96e-01 3.27e+01
  angle pdb=" C   GLU C 361 "
        pdb=" N   CYS C 362 "
        pdb=" CA  CYS C 362 "
      ideal   model   delta    sigma   weight residual
     120.87  128.95   -8.08 1.42e+00 4.96e-01 3.24e+01
  angle pdb=" N   VAL B  56 "
        pdb=" CA  VAL B  56 "
        pdb=" C   VAL B  56 "
      ideal   model   delta    sigma   weight residual
     112.29  109.10    3.19 9.40e-01 1.13e+00 1.15e+01
  angle pdb=" N   VAL A  56 "
        pdb=" CA  VAL A  56 "
        pdb=" C   VAL A  56 "
      ideal   model   delta    sigma   weight residual
     112.29  109.13    3.16 9.40e-01 1.13e+00 1.13e+01
  angle pdb=" N   ASN B  43 "
        pdb=" CA  ASN B  43 "
        pdb=" C   ASN B  43 "
      ideal   model   delta    sigma   weight residual
     109.81  116.44   -6.63 2.21e+00 2.05e-01 9.00e+00
  ... (remaining 16281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 6448
       17.15 -    34.29: 644
       34.29 -    51.44: 206
       51.44 -    68.59: 36
       68.59 -    85.73: 16
  Dihedral angle restraints: 7350
    sinusoidal: 3066
      harmonic: 4284
  Sorted by residual:
  dihedral pdb=" CA  ASN C  30 "
           pdb=" C   ASN C  30 "
           pdb=" N   TRP C  31 "
           pdb=" CA  TRP C  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.48  -22.52     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  ASN D  30 "
           pdb=" C   ASN D  30 "
           pdb=" N   TRP D  31 "
           pdb=" CA  TRP D  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.49  -22.51     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  ASP B   3 "
           pdb=" CB  ASP B   3 "
           pdb=" CG  ASP B   3 "
           pdb=" OD1 ASP B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.47   59.47     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 7347 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1174
       0.032 -    0.065: 418
       0.065 -    0.097: 130
       0.097 -    0.130: 48
       0.130 -    0.162: 2
  Chirality restraints: 1772
  Sorted by residual:
  chirality pdb=" CA  ASP D 372 "
            pdb=" N   ASP D 372 "
            pdb=" C   ASP D 372 "
            pdb=" CB  ASP D 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CA  ASP C 372 "
            pdb=" N   ASP C 372 "
            pdb=" C   ASP C 372 "
            pdb=" CB  ASP C 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.40e-01
  chirality pdb=" CA  SER D 359 "
            pdb=" N   SER D 359 "
            pdb=" C   SER D 359 "
            pdb=" CB  SER D 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1769 not shown)

  Planarity restraints: 2140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 360 "    0.053 2.00e-02 2.50e+03   5.76e-02 4.97e+01
        pdb=" CG  HIS C 360 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 360 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 360 "   -0.078 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 360 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 360 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 360 "   -0.053 2.00e-02 2.50e+03   5.76e-02 4.97e+01
        pdb=" CG  HIS D 360 "    0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 360 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 360 "    0.078 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 360 "    0.023 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 360 "   -0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 355 "    0.013 2.00e-02 2.50e+03   9.22e-03 1.70e+00
        pdb=" CG  TYR C 355 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 355 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 355 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 355 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 355 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 355 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 355 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2137 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 284
        2.68 -     3.24: 11768
        3.24 -     3.79: 18796
        3.79 -     4.35: 25270
        4.35 -     4.90: 41836
  Nonbonded interactions: 97954
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 219 "
            pdb="ZN    ZN C 701 "
     model   vdw
     2.127 2.230
  nonbonded pdb=" OD1 ASN D 219 "
            pdb="ZN    ZN D 701 "
     model   vdw
     2.127 2.230
  nonbonded pdb=" NH2 ARG D 191 "
            pdb=" O   THR C 331 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" O   THR D 331 "
            pdb=" NH2 ARG C 191 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" OG1 THR A  27 "
            pdb=" OG1 THR A  63 "
     model   vdw
     2.176 3.040
  ... (remaining 97949 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.920
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
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      :  0.005   0.207  12078  Z= 0.233
  Angle     :  0.609   8.115  16286  Z= 0.353
  Chirality :  0.039   0.162   1772
  Planarity :  0.003   0.058   2140
  Dihedral  : 15.450  85.735   4574
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  1.92 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 16.85 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1460
  helix:  1.33 (0.19), residues: 784
  sheet:  1.48 (0.54), residues: 108
  loop : -0.11 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 480 
 HIS   0.065   0.003   HIS D 360 
 PHE   0.015   0.001   PHE B  69 
 TYR   0.022   0.001   TYR C 355 
 ARG   0.005   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15653 (  592)
  hydrogen bonds       : angle       5.01665 ( 1734)
  metal coordination   : bond        0.18509 (    4)
  covalent geometry    : bond        0.00324 (12074)
  covalent geometry    : angle       0.60912 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 1.316 
Fit side-chains
REVERT: A   72 MET cc_start: 0.3886 (pp-130) cc_final: 0.3120 (mpm)
REVERT: A   95 LYS cc_start: 0.6430 (mptt) cc_final: 0.5967 (tppt)
REVERT: B   72 MET cc_start: 0.3888 (pp-130) cc_final: 0.3119 (mpm)
REVERT: B   95 LYS cc_start: 0.6427 (mptt) cc_final: 0.5969 (tppt)
  outliers start: 5
  outliers final: 2
  residues processed: 136
  average time/residue: 1.3506
  time to fit residues: 198.5791
Evaluate side-chains
  123 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain C residue  359 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 112 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:   30.0000
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
D 121 HIS
D 398 ASN
C 121 HIS
C 398 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.224512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.138610 restraints weight = 13092.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.65
r_work: 0.3449 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12078  Z= 0.174
  Angle     :  0.603  11.856  16286  Z= 0.323
  Chirality :  0.045   0.186   1772
  Planarity :  0.004   0.042   2140
  Dihedral  :  4.419  28.788   1606
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.88 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.00 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.22), residues: 1460
  helix:  1.25 (0.19), residues: 786
  sheet:  0.60 (0.62), residues: 82
  loop : -0.23 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 338 
 HIS   0.007   0.002   HIS D 561 
 PHE   0.020   0.002   PHE C 591 
 TYR   0.022   0.002   TYR C  49 
 ARG   0.004   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05254 (  592)
  hydrogen bonds       : angle       4.34078 ( 1734)
  metal coordination   : bond        0.00966 (    4)
  covalent geometry    : bond        0.00396 (12074)
  covalent geometry    : angle       0.60303 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 ASP cc_start: 0.3033 (OUTLIER) cc_final: 0.2523 (t0)
REVERT: A   73 MET cc_start: 0.4892 (ppp) cc_final: 0.3674 (ttt)
REVERT: A   95 LYS cc_start: 0.6775 (mptt) cc_final: 0.6215 (tppt)
REVERT: D  119 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7756 (tpp-160)
REVERT: D  225 MET cc_start: 0.9032 (mmm) cc_final: 0.8164 (mmm)
REVERT: D  470 MET cc_start: 0.2291 (OUTLIER) cc_final: 0.1673 (ppp)
REVERT: B    3 ASP cc_start: 0.3045 (OUTLIER) cc_final: 0.2534 (t0)
REVERT: B   73 MET cc_start: 0.4891 (ppp) cc_final: 0.3668 (ttt)
REVERT: B   95 LYS cc_start: 0.6791 (mptt) cc_final: 0.6238 (tppt)
REVERT: C  119 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7742 (tpp-160)
REVERT: C  225 MET cc_start: 0.9038 (mmm) cc_final: 0.8389 (mmt)
REVERT: C  470 MET cc_start: 0.2322 (OUTLIER) cc_final: 0.1701 (ppp)
  outliers start: 32
  outliers final: 12
  residues processed: 146
  average time/residue: 1.7510
  time to fit residues: 274.9978
Evaluate side-chains
  140 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  276 ASP
Chi-restraints excluded: chain D residue  402 MET
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  276 ASP
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  470 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 78 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 131 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
D 542 ASN
B 112 ASN
C 542 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.217900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.130891 restraints weight = 13253.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.47
r_work: 0.3269 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12078  Z= 0.274
  Angle     :  0.684  10.101  16286  Z= 0.368
  Chirality :  0.048   0.193   1772
  Planarity :  0.005   0.045   2140
  Dihedral  :  4.828  22.435   1604
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.77 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.30 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.22), residues: 1460
  helix:  0.49 (0.18), residues: 814
  sheet: -0.08 (0.61), residues: 82
  loop : -0.49 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 338 
 HIS   0.009   0.002   HIS C 561 
 PHE   0.021   0.002   PHE D 591 
 TYR   0.024   0.003   TYR D  49 
 ARG   0.005   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06354 (  592)
  hydrogen bonds       : angle       4.65693 ( 1734)
  metal coordination   : bond        0.00985 (    4)
  covalent geometry    : bond        0.00649 (12074)
  covalent geometry    : angle       0.68448 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 122
  time to evaluate  : 1.388 
Fit side-chains
REVERT: A    3 ASP cc_start: 0.3059 (OUTLIER) cc_final: 0.2671 (t70)
REVERT: A   95 LYS cc_start: 0.6707 (mptt) cc_final: 0.6288 (tptm)
REVERT: D  193 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7941 (mppt)
REVERT: D  194 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7676 (mpp80)
REVERT: D  225 MET cc_start: 0.9047 (mmm) cc_final: 0.8145 (mmm)
REVERT: D  470 MET cc_start: 0.2302 (OUTLIER) cc_final: 0.1907 (ppp)
REVERT: B    3 ASP cc_start: 0.3177 (OUTLIER) cc_final: 0.2793 (t70)
REVERT: B   95 LYS cc_start: 0.6709 (mptt) cc_final: 0.6286 (tptm)
REVERT: C  193 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7942 (mppt)
REVERT: C  194 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7677 (mpp80)
REVERT: C  225 MET cc_start: 0.9051 (mmm) cc_final: 0.8154 (mmm)
REVERT: C  470 MET cc_start: 0.2220 (OUTLIER) cc_final: 0.1871 (ppp)
  outliers start: 44
  outliers final: 21
  residues processed: 150
  average time/residue: 1.5439
  time to fit residues: 248.8760
Evaluate side-chains
  143 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 130 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 118 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.221139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.131589 restraints weight = 13147.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.53
r_work: 0.3335 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12078  Z= 0.121
  Angle     :  0.540   9.151  16286  Z= 0.287
  Chirality :  0.042   0.180   1772
  Planarity :  0.004   0.038   2140
  Dihedral  :  4.369  21.991   1604
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.01 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.54 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.22), residues: 1460
  helix:  0.79 (0.18), residues: 816
  sheet: -0.20 (0.55), residues: 94
  loop : -0.43 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 338 
 HIS   0.006   0.001   HIS C 561 
 PHE   0.017   0.001   PHE C  11 
 TYR   0.019   0.002   TYR D  49 
 ARG   0.006   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  592)
  hydrogen bonds       : angle       4.27884 ( 1734)
  metal coordination   : bond        0.00344 (    4)
  covalent geometry    : bond        0.00255 (12074)
  covalent geometry    : angle       0.54048 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.5238 (ppp) cc_final: 0.3570 (ttt)
REVERT: A   95 LYS cc_start: 0.6719 (mptt) cc_final: 0.6222 (tptm)
REVERT: D   18 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7883 (ttm-80)
REVERT: D  193 LYS cc_start: 0.8416 (mppt) cc_final: 0.8191 (mtmm)
REVERT: D  194 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7393 (mpp80)
REVERT: D  470 MET cc_start: 0.2160 (OUTLIER) cc_final: 0.1784 (ppp)
REVERT: B   73 MET cc_start: 0.5243 (ppp) cc_final: 0.3566 (ttt)
REVERT: B   95 LYS cc_start: 0.6708 (mptt) cc_final: 0.6217 (tptm)
REVERT: C   18 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7884 (ttm-80)
REVERT: C  193 LYS cc_start: 0.8414 (mppt) cc_final: 0.8187 (mtmm)
REVERT: C  194 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7393 (mpp80)
REVERT: C  470 MET cc_start: 0.2158 (OUTLIER) cc_final: 0.1694 (ppp)
  outliers start: 32
  outliers final: 12
  residues processed: 139
  average time/residue: 1.5734
  time to fit residues: 234.0034
Evaluate side-chains
  133 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  439 MET
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  470 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 128 optimal weight:   20.0000
   chunk 82 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0570
   chunk 25 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 108 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 72 optimal weight:   20.0000
   chunk 59 optimal weight:    8.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.222624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131939 restraints weight = 13230.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.26
r_work: 0.3398 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12078  Z= 0.113
  Angle     :  0.514   8.829  16286  Z= 0.272
  Chirality :  0.041   0.169   1772
  Planarity :  0.004   0.034   2140
  Dihedral  :  4.132  21.160   1604
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.22 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.47 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.23), residues: 1460
  helix:  1.09 (0.19), residues: 802
  sheet: -0.12 (0.56), residues: 94
  loop : -0.27 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 338 
 HIS   0.006   0.001   HIS C 561 
 PHE   0.018   0.001   PHE D  11 
 TYR   0.035   0.002   TYR D  49 
 ARG   0.004   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  592)
  hydrogen bonds       : angle       4.16261 ( 1734)
  metal coordination   : bond        0.00268 (    4)
  covalent geometry    : bond        0.00237 (12074)
  covalent geometry    : angle       0.51385 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A   73 MET cc_start: 0.4763 (ppp) cc_final: 0.3969 (ttt)
REVERT: A   95 LYS cc_start: 0.6802 (mptt) cc_final: 0.6208 (tptm)
REVERT: D   18 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7963 (ttm-80)
REVERT: D  119 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7743 (tpp-160)
REVERT: D  194 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7418 (mpp80)
REVERT: D  470 MET cc_start: 0.2183 (OUTLIER) cc_final: 0.1771 (ppp)
REVERT: B   73 MET cc_start: 0.4900 (ppp) cc_final: 0.4046 (ttt)
REVERT: B   95 LYS cc_start: 0.6806 (mptt) cc_final: 0.6209 (tptm)
REVERT: C   16 TYR cc_start: 0.7466 (t80) cc_final: 0.7179 (t80)
REVERT: C   18 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7971 (ttm-80)
REVERT: C  119 ARG cc_start: 0.7971 (mmt90) cc_final: 0.7737 (tpp-160)
REVERT: C  194 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7413 (mpp80)
REVERT: C  470 MET cc_start: 0.2182 (OUTLIER) cc_final: 0.1775 (ppp)
  outliers start: 28
  outliers final: 17
  residues processed: 141
  average time/residue: 1.5762
  time to fit residues: 237.7907
Evaluate side-chains
  147 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  439 MET
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 139 optimal weight:    0.5980
   chunk 90 optimal weight:    9.9990
   chunk 134 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.221377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.148478 restraints weight = 13103.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.33
r_work: 0.3399 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12078  Z= 0.120
  Angle     :  0.539  10.757  16286  Z= 0.283
  Chirality :  0.041   0.169   1772
  Planarity :  0.004   0.033   2140
  Dihedral  :  4.128  21.244   1604
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.08 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.92 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.23), residues: 1460
  helix:  1.12 (0.19), residues: 796
  sheet: -0.14 (0.56), residues: 94
  loop : -0.18 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.006   0.001   HIS C 561 
 PHE   0.018   0.001   PHE C  11 
 TYR   0.035   0.002   TYR C  49 
 ARG   0.004   0.000   ARG D 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  592)
  hydrogen bonds       : angle       4.20150 ( 1734)
  metal coordination   : bond        0.00317 (    4)
  covalent geometry    : bond        0.00260 (12074)
  covalent geometry    : angle       0.53921 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.369 
Fit side-chains
REVERT: A    3 ASP cc_start: 0.3250 (OUTLIER) cc_final: 0.2833 (t70)
REVERT: A   73 MET cc_start: 0.4598 (ppp) cc_final: 0.3498 (ttt)
REVERT: A   95 LYS cc_start: 0.6842 (mptt) cc_final: 0.6264 (tptm)
REVERT: D   16 TYR cc_start: 0.7574 (t80) cc_final: 0.7303 (t80)
REVERT: D   18 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7972 (ttm-80)
REVERT: D  119 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7757 (tpp-160)
REVERT: D  194 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7416 (mpp80)
REVERT: D  470 MET cc_start: 0.2411 (OUTLIER) cc_final: 0.1944 (ppp)
REVERT: B    3 ASP cc_start: 0.3240 (OUTLIER) cc_final: 0.2822 (t70)
REVERT: B   73 MET cc_start: 0.4602 (ppp) cc_final: 0.3500 (ttt)
REVERT: B   95 LYS cc_start: 0.6855 (mptt) cc_final: 0.6281 (tptm)
REVERT: C   18 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7984 (ttm-80)
REVERT: C  119 ARG cc_start: 0.7982 (mmt90) cc_final: 0.7752 (tpp-160)
REVERT: C  194 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7422 (mpp80)
REVERT: C  325 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8209 (mtm)
REVERT: C  470 MET cc_start: 0.2284 (OUTLIER) cc_final: 0.1806 (ppp)
  outliers start: 33
  outliers final: 17
  residues processed: 149
  average time/residue: 1.5903
  time to fit residues: 253.4745
Evaluate side-chains
  152 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  439 MET
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  325 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0470
   chunk 134 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    1.0280

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.219957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.144515 restraints weight = 13035.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 3.70
r_work: 0.3369 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12078  Z= 0.133
  Angle     :  0.556  10.269  16286  Z= 0.296
  Chirality :  0.042   0.184   1772
  Planarity :  0.004   0.034   2140
  Dihedral  :  4.172  21.695   1604
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.29 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.16 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1460
  helix:  1.08 (0.19), residues: 808
  sheet: -0.26 (0.55), residues: 94
  loop : -0.26 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.006   0.001   HIS D 561 
 PHE   0.019   0.001   PHE D  11 
 TYR   0.034   0.002   TYR C  49 
 ARG   0.003   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  592)
  hydrogen bonds       : angle       4.31819 ( 1734)
  metal coordination   : bond        0.00390 (    4)
  covalent geometry    : bond        0.00294 (12074)
  covalent geometry    : angle       0.55614 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A   73 MET cc_start: 0.4640 (ppp) cc_final: 0.3493 (ttt)
REVERT: A   95 LYS cc_start: 0.6835 (mptt) cc_final: 0.6228 (tptm)
REVERT: D   16 TYR cc_start: 0.7472 (t80) cc_final: 0.7256 (t80)
REVERT: D   18 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7936 (ttm-80)
REVERT: D   24 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7087 (mm-30)
REVERT: D  119 ARG cc_start: 0.7996 (mmt90) cc_final: 0.7746 (tpp-160)
REVERT: D  194 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7479 (mpp80)
REVERT: D  470 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.1960 (ppp)
REVERT: B   95 LYS cc_start: 0.6865 (mptt) cc_final: 0.6254 (tptm)
REVERT: C   16 TYR cc_start: 0.7475 (t80) cc_final: 0.7255 (t80)
REVERT: C   18 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7956 (ttm-80)
REVERT: C  119 ARG cc_start: 0.7989 (mmt90) cc_final: 0.7732 (tpp-160)
REVERT: C  194 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7487 (mpp80)
REVERT: C  470 MET cc_start: 0.2381 (OUTLIER) cc_final: 0.1964 (ppp)
  outliers start: 32
  outliers final: 18
  residues processed: 144
  average time/residue: 1.6792
  time to fit residues: 260.7568
Evaluate side-chains
  150 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  439 MET
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 128 optimal weight:    8.9990
   chunk 109 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 105 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.222119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132733 restraints weight = 13271.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.51
r_work: 0.3368 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12078  Z= 0.119
  Angle     :  0.553   9.753  16286  Z= 0.286
  Chirality :  0.041   0.179   1772
  Planarity :  0.004   0.033   2140
  Dihedral  :  4.104  21.481   1604
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.01 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.01 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.23), residues: 1460
  helix:  1.12 (0.19), residues: 808
  sheet: -0.22 (0.56), residues: 94
  loop : -0.24 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.007   0.001   HIS D 561 
 PHE   0.020   0.001   PHE C  11 
 TYR   0.032   0.002   TYR C  49 
 ARG   0.003   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03886 (  592)
  hydrogen bonds       : angle       4.15877 ( 1734)
  metal coordination   : bond        0.00334 (    4)
  covalent geometry    : bond        0.00259 (12074)
  covalent geometry    : angle       0.55309 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.6897 (mptt) cc_final: 0.6289 (tptm)
REVERT: D   16 TYR cc_start: 0.7472 (t80) cc_final: 0.7207 (t80)
REVERT: D  119 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7753 (tpp-160)
REVERT: D  194 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7521 (mpp80)
REVERT: D  470 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.2040 (ppp)
REVERT: D  518 MET cc_start: 0.3998 (ppp) cc_final: 0.3607 (pmm)
REVERT: B    3 ASP cc_start: 0.3378 (OUTLIER) cc_final: 0.2963 (t70)
REVERT: B   73 MET cc_start: 0.5484 (ppp) cc_final: 0.3815 (ttt)
REVERT: B   95 LYS cc_start: 0.6904 (mptt) cc_final: 0.6299 (tptm)
REVERT: C   24 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7115 (mm-30)
REVERT: C  119 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7742 (tpp-160)
REVERT: C  194 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7529 (mpp80)
REVERT: C  470 MET cc_start: 0.2440 (OUTLIER) cc_final: 0.1994 (ppp)
  outliers start: 31
  outliers final: 15
  residues processed: 143
  average time/residue: 1.5239
  time to fit residues: 233.8061
Evaluate side-chains
  144 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain D residue  551 PHE
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  551 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 124 optimal weight:    0.6980
   chunk 123 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.221991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.131106 restraints weight = 13183.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.95
r_work: 0.3415 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12078  Z= 0.121
  Angle     :  0.559  13.048  16286  Z= 0.288
  Chirality :  0.042   0.221   1772
  Planarity :  0.004   0.033   2140
  Dihedral  :  4.119  21.503   1604
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.29 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.55 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.23), residues: 1460
  helix:  1.08 (0.19), residues: 814
  sheet: -0.27 (0.56), residues: 94
  loop : -0.29 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.008   0.001   HIS C 561 
 PHE   0.020   0.001   PHE D  11 
 TYR   0.032   0.002   TYR D  49 
 ARG   0.003   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  592)
  hydrogen bonds       : angle       4.21360 ( 1734)
  metal coordination   : bond        0.00319 (    4)
  covalent geometry    : bond        0.00265 (12074)
  covalent geometry    : angle       0.55850 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 ASP cc_start: 0.3176 (OUTLIER) cc_final: 0.2792 (t70)
REVERT: A   73 MET cc_start: 0.5328 (ppp) cc_final: 0.3430 (ttt)
REVERT: A   95 LYS cc_start: 0.6841 (mptt) cc_final: 0.6219 (tptm)
REVERT: D  119 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7735 (tpp-160)
REVERT: D  194 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7455 (mpp80)
REVERT: D  470 MET cc_start: 0.2411 (OUTLIER) cc_final: 0.1986 (ppp)
REVERT: D  518 MET cc_start: 0.3998 (ppp) cc_final: 0.3606 (pmm)
REVERT: B    3 ASP cc_start: 0.3216 (OUTLIER) cc_final: 0.2807 (t70)
REVERT: B   73 MET cc_start: 0.5413 (ppp) cc_final: 0.2982 (ttt)
REVERT: B   95 LYS cc_start: 0.6866 (mptt) cc_final: 0.6244 (tptm)
REVERT: C   24 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7137 (mm-30)
REVERT: C  119 ARG cc_start: 0.7956 (mmt90) cc_final: 0.7727 (tpp-160)
REVERT: C  194 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7459 (mpp80)
REVERT: C  470 MET cc_start: 0.2352 (OUTLIER) cc_final: 0.2025 (ppp)
  outliers start: 26
  outliers final: 16
  residues processed: 144
  average time/residue: 1.4689
  time to fit residues: 227.0775
Evaluate side-chains
  145 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  194 ARG
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  470 MET
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain D residue  551 PHE
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  194 ARG
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  470 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  551 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 135 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 117 optimal weight:    0.4980
   chunk 42 optimal weight:    0.0270
   chunk 82 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.223318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132885 restraints weight = 13089.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.25
r_work: 0.3414 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12078  Z= 0.109
  Angle     :  0.574  14.798  16286  Z= 0.291
  Chirality :  0.041   0.228   1772
  Planarity :  0.003   0.031   2140
  Dihedral  :  4.036  21.125   1604
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.08 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.17 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.23), residues: 1460
  helix:  1.19 (0.19), residues: 804
  sheet: -0.10 (0.57), residues: 94
  loop : -0.22 (0.28), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.007   0.001   HIS D 561 
 PHE   0.020   0.001   PHE C  11 
 TYR   0.040   0.002   TYR C  16 
 ARG   0.003   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  592)
  hydrogen bonds       : angle       4.16987 ( 1734)
  metal coordination   : bond        0.00209 (    4)
  covalent geometry    : bond        0.00231 (12074)
  covalent geometry    : angle       0.57368 (16286)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 ASP cc_start: 0.3236 (OUTLIER) cc_final: 0.2830 (t70)
REVERT: A   73 MET cc_start: 0.5002 (ppp) cc_final: 0.2865 (ttt)
REVERT: A   95 LYS cc_start: 0.6850 (mptt) cc_final: 0.6185 (tptm)
REVERT: D  518 MET cc_start: 0.4070 (ppp) cc_final: 0.3685 (pmm)
REVERT: B   73 MET cc_start: 0.5329 (ppp) cc_final: 0.4079 (ttt)
REVERT: B   95 LYS cc_start: 0.6852 (mptt) cc_final: 0.6183 (tptm)
REVERT: C   24 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7102 (mm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 140
  average time/residue: 1.4914
  time to fit residues: 224.4907
Evaluate side-chains
  138 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  244 LYS
Chi-restraints excluded: chain D residue  427 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  521 MET
Chi-restraints excluded: chain D residue  551 PHE
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  244 LYS
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  551 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 116 optimal weight:    0.3980
   chunk 125 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 90 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0170
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.223420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.133456 restraints weight = 13162.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.93
r_work: 0.3450 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  12078  Z= 0.109
  Angle     :  0.580  15.779  16286  Z= 0.289
  Chirality :  0.041   0.210   1772
  Planarity :  0.003   0.031   2140
  Dihedral  :  4.002  20.182   1604
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.95 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 19.78 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.23), residues: 1460
  helix:  1.29 (0.19), residues: 794
  sheet: -0.30 (0.56), residues: 98
  loop : -0.11 (0.28), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 338 
 HIS   0.006   0.001   HIS C 561 
 PHE   0.019   0.001   PHE C  11 
 TYR   0.043   0.002   TYR C  16 
 ARG   0.002   0.000   ARG D 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03530 (  592)
  hydrogen bonds       : angle       4.11195 ( 1734)
  metal coordination   : bond        0.00201 (    4)
  covalent geometry    : bond        0.00232 (12074)
  covalent geometry    : angle       0.57964 (16286)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11836.71 seconds
wall clock time: 202 minutes 26.21 seconds (12146.21 seconds total)