Starting phenix.real_space_refine
on Fri Jul  3 03:51:33 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7das_30626/07_2026/7das_30626.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      28      5.16       5
     C    7232      2.51       5
     N    1847      2.21       5
     O    2430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11603
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5418
          Classifications: {'peptide': 674}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 645}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 671, 5393
          Classifications: {'peptide': 671}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 792
          Classifications: {'RNA': 66}
          Modifications used: {'rna3p_pur': 32, 'rna3p_pyr': 34}
          Link IDs: {'rna3p': 65}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 707
          Unresolved non-hydrogen angles: 1118
          Unresolved non-hydrogen dihedrals: 492
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'  U%rna3p_pyr:plan': 12, '  G%rna3p_pur:plan': 17, '  G%rna3p_pur:plan2': 17, '  A%rna3p_pur:plan': 15, '  A%rna3p_pur:plan2': 15, '  C%rna3p_pyr:plan': 22, '  C%rna3p_pyr:plan2': 22}
          Unresolved non-hydrogen planarities: 717
  Time building chain proxies: 2.95, per 1000 atoms: 0.25
  Number of scatterers: 11603
  At special positions: 0
  Unit cell: (110.7, 110.7, 136.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      66     15.00
     O    2430      8.00
     N    1847      7.00
     C    7232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  38 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 678 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 652 " - pdb=" SG  CYS A 697 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  29 " - pdb=" SG  CYS B  38 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  96 " - pdb=" SG  CYS B 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 650 " - pdb=" SG  CYS B 678 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 652 " - pdb=" SG  CYS B 697 " distance=2.03

  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
      
  Atom "ATOM  10938  O4'   U C  19 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 522.7 milliseconds
  

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2586

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 14 sheets defined
      11.6% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 92 through 99
      removed outlier: 4.230A  pdb=" N   CYS A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 3.578A  pdb=" N   GLY A 196 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 247
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.746A  pdb=" N   LYS A 273 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TRP A 274 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
    Processing helix  chain 'A' and resid 450 through 454
      removed outlier: 3.817A  pdb=" N   TRP A 453 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 3.657A  pdb=" N   PHE A 631 " --> pdb=" O   GLU A 627 " (cutoff:3.500A)
      Proline residue:  A 633  - end of helix
    Processing helix  chain 'A' and resid 651 through 665
      removed outlier: 6.436A  pdb=" N   TRP A 657 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE A 658 " --> pdb=" O   SER A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'B' and resid 92 through 99
      removed outlier: 4.230A  pdb=" N   CYS B  96 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B  97 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.578A  pdb=" N   GLY B 196 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 247
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.747A  pdb=" N   LYS B 273 " --> pdb=" O   SER B 270 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TRP B 274 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 406
    Processing helix  chain 'B' and resid 450 through 454
      removed outlier: 3.818A  pdb=" N   TRP B 453 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 547
    Processing helix  chain 'B' and resid 627 through 636
      removed outlier: 3.657A  pdb=" N   PHE B 631 " --> pdb=" O   GLU B 627 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 651 through 665
      removed outlier: 6.436A  pdb=" N   TRP B 657 " --> pdb=" O   GLU B 653 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE B 658 " --> pdb=" O   SER B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 692
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37
      removed outlier: 3.515A  pdb=" N   LEU A  57 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU A 153 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU A 177 " --> pdb=" O   ASP A 204 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LEU A 227 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
      removed outlier: 3.539A  pdb=" N   LEU A 187 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200
    Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281
      removed outlier: 7.309A  pdb=" N   LEU A 304 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LEU A 328 " --> pdb=" O   ASN A 362 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU A 385 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A 413 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LEU A 437 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   ILE A 462 " --> pdb=" O   MET A 487 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447
      removed outlier: 7.048A  pdb=" N   GLN A 446 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 537
      removed outlier: 6.943A  pdb=" N   LEU A 536 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE A 592 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 616 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37
      removed outlier: 3.515A  pdb=" N   LEU B  57 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B 153 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 177 " --> pdb=" O   ASP B 204 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B 227 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 187
      removed outlier: 3.539A  pdb=" N   LEU B 187 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 200
    Processing sheet with id=AB2, first strand: chain 'B' and resid 279 through 281
      removed outlier: 7.309A  pdb=" N   LEU B 304 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU B 328 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU B 385 " --> pdb=" O   ASN B 414 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B 413 " --> pdb=" O   ASP B 438 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LEU B 437 " --> pdb=" O   TYR B 463 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   ILE B 462 " --> pdb=" O   MET B 487 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 447
      removed outlier: 7.048A  pdb=" N   GLN B 446 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 535 through 537
      removed outlier: 6.944A  pdb=" N   LEU B 536 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE B 592 " --> pdb=" O   ASN B 617 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU B 616 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    240 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3345
        1.33 -     1.46: 2221
        1.46 -     1.58: 6164
        1.58 -     1.70: 129
        1.70 -     1.82: 36
  Bond restraints: 11895
  Sorted by residual:
  bond pdb=" N   PRO B 579 "
       pdb=" CD  PRO B 579 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.97e+01
  bond pdb=" N   PRO A 579 "
       pdb=" CD  PRO A 579 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.96e+01
  bond pdb=" O3'   G C  10 "
       pdb=" P     A C  11 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.50e-02 4.44e+03 1.41e+01
  bond pdb=" O3'   A C  34 "
       pdb=" P     C C  35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.50e-02 4.44e+03 1.40e+01
  bond pdb=" O3'   G C  13 "
       pdb=" P     G C  14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.50e-02 4.44e+03 1.32e+01
  ... (remaining 11890 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 15723
        2.29 -     4.58: 510
        4.58 -     6.87: 53
        6.87 -     9.16: 8
        9.16 -    11.45: 5
  Bond angle restraints: 16299
  Sorted by residual:
  angle pdb=" N   HIS B 683 "
        pdb=" CA  HIS B 683 "
        pdb=" C   HIS B 683 "
      ideal   model   delta    sigma   weight residual
     112.38  103.04    9.34 1.22e+00 6.72e-01 5.86e+01
  angle pdb=" N   HIS A 683 "
        pdb=" CA  HIS A 683 "
        pdb=" C   HIS A 683 "
      ideal   model   delta    sigma   weight residual
     112.38  103.06    9.32 1.22e+00 6.72e-01 5.83e+01
  angle pdb=" O3'   G C  13 "
        pdb=" C3'   G C  13 "
        pdb=" C2'   G C  13 "
      ideal   model   delta    sigma   weight residual
     113.70  125.15  -11.45 1.50e+00 4.44e-01 5.83e+01
  angle pdb=" C3'   G C  18 "
        pdb=" C2'   G C  18 "
        pdb=" O2'   G C  18 "
      ideal   model   delta    sigma   weight residual
     110.70  120.23   -9.53 1.50e+00 4.44e-01 4.03e+01
  angle pdb=" C4'   G C 238 "
        pdb=" C3'   G C 238 "
        pdb=" O3'   G C 238 "
      ideal   model   delta    sigma   weight residual
     113.00  122.27   -9.27 1.50e+00 4.44e-01 3.82e+01
  ... (remaining 16294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 7153
       33.25 -    66.49: 222
       66.49 -    99.74: 35
       99.74 -   132.99: 0
      132.99 -   166.23: 1
  Dihedral angle restraints: 7411
    sinusoidal: 3448
      harmonic: 3963
  Sorted by residual:
  dihedral pdb=" C5'   U C 259 "
           pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" O3'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  166.04  -84.04     1      8.00e+00 1.56e-02 1.34e+02
  dihedral pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" C2'   U C 259 "
           pdb=" C1'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00  -40.89   76.89     1      8.00e+00 1.56e-02 1.16e+02
  dihedral pdb=" O4'   U C 259 "
           pdb=" C4'   U C 259 "
           pdb=" C3'   U C 259 "
           pdb=" C2'   U C 259 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   37.98  -72.98     1      8.00e+00 1.56e-02 1.06e+02
  ... (remaining 7408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.177: 1947
       0.177 -    0.355: 41
       0.355 -    0.532: 3
       0.532 -    0.710: 1
       0.710 -    0.887: 2
  Chirality restraints: 1994
  Sorted by residual:
  chirality pdb=" C3'   G C  13 "
            pdb=" C4'   G C  13 "
            pdb=" O3'   G C  13 "
            pdb=" C2'   G C  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.59   -0.89 2.00e-01 2.50e+01 1.97e+01
  chirality pdb=" C3'   G C  18 "
            pdb=" C4'   G C  18 "
            pdb=" O3'   G C  18 "
            pdb=" C2'   G C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.69   -0.78 2.00e-01 2.50e+01 1.54e+01
  chirality pdb=" C2'   G C  18 "
            pdb=" C3'   G C  18 "
            pdb=" O2'   G C  18 "
            pdb=" C1'   G C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.08   -0.68 2.00e-01 2.50e+01 1.15e+01
  ... (remaining 1991 not shown)

  Planarity restraints: 1922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 513 "   -0.025 2.00e-02 2.50e+03   5.21e-02 2.71e+01
        pdb=" C   ASP B 513 "    0.090 2.00e-02 2.50e+03
        pdb=" O   ASP B 513 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   LEU B 514 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 513 "    0.025 2.00e-02 2.50e+03   5.19e-02 2.70e+01
        pdb=" C   ASP A 513 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   ASP A 513 "    0.034 2.00e-02 2.50e+03
        pdb=" N   LEU A 514 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 678 "   -0.025 2.00e-02 2.50e+03   5.12e-02 2.62e+01
        pdb=" C   CYS B 678 "    0.089 2.00e-02 2.50e+03
        pdb=" O   CYS B 678 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   ASN B 679 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1919 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 4
        2.18 -     2.86: 4267
        2.86 -     3.54: 15216
        3.54 -     4.22: 26677
        4.22 -     4.90: 45075
  Nonbonded interactions: 91239
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 518 "
            pdb=" O4'   U C  19 "
     model   vdw
     1.496 3.120
  nonbonded pdb=" OD1 ASN B 542 "
            pdb=" O2'   U C  17 "
     model   vdw
     1.898 3.040
  nonbonded pdb=" ND2 ASN B 518 "
            pdb=" C1'   U C  19 "
     model   vdw
     1.977 3.550
  nonbonded pdb=" CG  ASN B 518 "
            pdb=" O4'   U C  19 "
     model   vdw
     2.175 3.270
  nonbonded pdb=" O   PRO A 316 "
            pdb=" NE1 TRP A 354 "
     model   vdw
     2.213 3.120
  ... (remaining 91234 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 24 through 697)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.360
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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      :  0.006   0.062  11903  Z= 0.342
  Angle     :  0.919  11.450  16315  Z= 0.594
  Chirality :  0.071   0.887   1994
  Planarity :  0.005   0.052   1922
  Dihedral  : 16.280 166.233   4801
  Min Nonbonded Distance : 1.496

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.93 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.20), residues: 1337
  helix: -3.01 (0.41), residues: 88
  sheet: -2.94 (0.34), residues: 192
  loop : -2.69 (0.17), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 644 
 TYR   0.017   0.002   TYR B 469 
 PHE   0.018   0.001   PHE B 558 
 TRP   0.012   0.001   TRP B 547 
 HIS   0.005   0.001   HIS A 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00564 /  0.34 (11895)
  covalent geometry    : angle       0.91787 /  0.59 (16299)
  SS BOND              : bond        0.01190 /  0.62 (    8)
  SS BOND              : angle       1.62012 /  0.82 (   16)
  hydrogen bonds       : bond        0.23531 / 14.87 (  100)
  hydrogen bonds       : angle      10.52559 /  6.89 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  643 MET cc_start: 0.7939 (ttm) cc_final: 0.7446 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1245
  time to fit residues: 18.4319
Evaluate side-chains
  39 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  62 ASN
A 110 ASN
A 134 ASN
A 170 GLN
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 395 GLN
A 446 GLN
A 467 ASN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 HIS
A 573 ASN
A 585 ASN
A 610 GLN
A 621 ASN
A 646 ASN
A 679 ASN
B  61 HIS
B  62 ASN
B 109 HIS
B 110 ASN
B 134 ASN
B 149 ASN
B 170 GLN
B 395 GLN
B 446 GLN
B 451 GLN
B 467 ASN
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 HIS
B 573 ASN
B 585 ASN
B 610 GLN
B 621 ASN
B 639 ASN
B 646 ASN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.074738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.061615 restraints weight = 41067.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.063158 restraints weight = 21443.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.064183 restraints weight = 13740.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.064828 restraints weight = 10116.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.065292 restraints weight = 8264.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11903  Z= 0.246
  Angle     :  0.672  10.732  16315  Z= 0.345
  Chirality :  0.044   0.145   1994
  Planarity :  0.005   0.043   1922
  Dihedral  : 12.805 163.167   2143
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.66 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.22), residues: 1337
  helix: -1.33 (0.52), residues: 100
  sheet: -2.70 (0.38), residues: 169
  loop : -2.05 (0.18), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 326 
 TYR   0.016   0.002   TYR A 469 
 PHE   0.017   0.002   PHE B 460 
 TRP   0.014   0.002   TRP B 547 
 HIS   0.005   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00568 /  0.25 (11895)
  covalent geometry    : angle       0.67101 /  0.34 (16299)
  SS BOND              : bond        0.00568 /  0.33 (    8)
  SS BOND              : angle       1.21744 /  0.61 (   16)
  hydrogen bonds       : bond        0.04487 /  2.78 (  100)
  hydrogen bonds       : angle       6.63653 /  4.47 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 34
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  538 PHE cc_start: 0.8557 (t80) cc_final: 0.8287 (t80)
REVERT: B   24 TYR cc_start: 0.4457 (OUTLIER) cc_final: 0.4076 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 49
  average time/residue: 0.0972
  time to fit residues: 7.3449
Evaluate side-chains
  33 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0050
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.9198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 HIS
A 146 ASN
A 260 GLN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
B 146 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.074063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.060724 restraints weight = 42251.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.062323 restraints weight = 21814.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.063396 restraints weight = 13854.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.064106 restraints weight = 10121.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.064467 restraints weight = 8170.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11903  Z= 0.175
  Angle     :  0.562   8.026  16315  Z= 0.291
  Chirality :  0.042   0.152   1994
  Planarity :  0.004   0.043   1922
  Dihedral  : 12.490 164.410   2143
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.97 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.23), residues: 1337
  helix: -1.32 (0.52), residues: 106
  sheet: -2.45 (0.41), residues: 174
  loop : -1.75 (0.19), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 326 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.014   0.001   TRP B 274 
 HIS   0.002   0.001   HIS B  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 (11895)
  covalent geometry    : angle       0.56138 /  0.29 (16299)
  SS BOND              : bond        0.00807 /  0.56 (    8)
  SS BOND              : angle       0.92799 /  0.47 (   16)
  hydrogen bonds       : bond        0.04032 /  2.50 (  100)
  hydrogen bonds       : angle       5.99973 /  4.12 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8617 (tt)
REVERT: B   24 TYR cc_start: 0.4465 (OUTLIER) cc_final: 0.3880 (t80)
REVERT: B  484 GLN cc_start: 0.7818 (tt0) cc_final: 0.7271 (tm-30)
  outliers start: 21
  outliers final: 10
  residues processed: 52
  average time/residue: 0.0757
  time to fit residues: 6.7893
Evaluate side-chains
  38 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0170
   chunk 53 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.2822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS
B 682 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.074419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.061191 restraints weight = 41702.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.062827 restraints weight = 21272.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.063895 restraints weight = 13399.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.064627 restraints weight = 9771.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.065059 restraints weight = 7829.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11903  Z= 0.125
  Angle     :  0.523  11.755  16315  Z= 0.265
  Chirality :  0.040   0.181   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 12.253 163.684   2143
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.24 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.23), residues: 1337
  helix: -1.01 (0.56), residues: 100
  sheet: -2.31 (0.42), residues: 174
  loop : -1.52 (0.19), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 326 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.009   0.001   PHE B 460 
 TRP   0.009   0.001   TRP B 274 
 HIS   0.017   0.001   HIS B 682 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.12 (11895)
  covalent geometry    : angle       0.52305 /  0.26 (16299)
  SS BOND              : bond        0.00855 /  0.60 (    8)
  SS BOND              : angle       0.84071 /  0.41 (   16)
  hydrogen bonds       : bond        0.03249 /  1.97 (  100)
  hydrogen bonds       : angle       5.69790 /  3.91 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7138 (p90)
REVERT: A  512 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: B   24 TYR cc_start: 0.4484 (OUTLIER) cc_final: 0.3816 (t80)
REVERT: B  484 GLN cc_start: 0.7748 (tt0) cc_final: 0.7363 (mt0)
  outliers start: 21
  outliers final: 11
  residues processed: 53
  average time/residue: 0.0731
  time to fit residues: 6.5771
Evaluate side-chains
  39 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 25
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 134 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.072018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.059161 restraints weight = 42339.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.060614 restraints weight = 22934.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.061591 restraints weight = 15059.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.062235 restraints weight = 11236.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.062646 restraints weight = 9166.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  11903  Z= 0.245
  Angle     :  0.628   7.406  16315  Z= 0.323
  Chirality :  0.044   0.205   1994
  Planarity :  0.004   0.041   1922
  Dihedral  : 12.678 159.667   2143
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.52 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.51 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.23), residues: 1337
  helix: -1.21 (0.52), residues: 106
  sheet: -2.71 (0.39), residues: 189
  loop : -1.54 (0.20), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 326 
 TYR   0.015   0.002   TYR A 469 
 PHE   0.017   0.002   PHE B 460 
 TRP   0.015   0.002   TRP B 274 
 HIS   0.004   0.001   HIS A 540 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.24 (11895)
  covalent geometry    : angle       0.62794 /  0.32 (16299)
  SS BOND              : bond        0.00627 /  0.39 (    8)
  SS BOND              : angle       0.95595 /  0.49 (   16)
  hydrogen bonds       : bond        0.04383 /  2.76 (  100)
  hydrogen bonds       : angle       6.03599 /  4.17 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 25
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6973 (p90)
REVERT: A  512 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (tt)
REVERT: B   24 TYR cc_start: 0.4334 (OUTLIER) cc_final: 0.3604 (t80)
REVERT: B  508 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7668 (t0)
  outliers start: 29
  outliers final: 16
  residues processed: 52
  average time/residue: 0.0837
  time to fit residues: 7.1279
Evaluate side-chains
  41 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 21
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  508 ASN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 129 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 136 optimal weight:   20.0000
   chunk 138 optimal weight:   20.0000
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.073476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.060504 restraints weight = 41433.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.062087 restraints weight = 21452.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.063137 restraints weight = 13643.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.063845 restraints weight = 9971.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.064321 restraints weight = 8025.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11903  Z= 0.123
  Angle     :  0.514   7.831  16315  Z= 0.263
  Chirality :  0.040   0.158   1994
  Planarity :  0.004   0.039   1922
  Dihedral  : 12.467 158.917   2143
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.83 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.24), residues: 1337
  helix: -1.07 (0.53), residues: 106
  sheet: -2.56 (0.40), residues: 186
  loop : -1.38 (0.20), residues: 1045

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 504 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.007   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS A 540 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 (11895)
  covalent geometry    : angle       0.51358 /  0.26 (16299)
  SS BOND              : bond        0.00428 /  0.27 (    8)
  SS BOND              : angle       0.83592 /  0.41 (   16)
  hydrogen bonds       : bond        0.03314 /  2.08 (  100)
  hydrogen bonds       : angle       5.63863 /  3.91 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 28
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6461 (p90)
REVERT: B   24 TYR cc_start: 0.4411 (OUTLIER) cc_final: 0.3830 (t80)
REVERT: B   26 GLN cc_start: 0.8077 (mp10) cc_final: 0.7751 (mp10)
REVERT: B  484 GLN cc_start: 0.7897 (tt0) cc_final: 0.7200 (tm-30)
  outliers start: 28
  outliers final: 19
  residues processed: 53
  average time/residue: 0.0728
  time to fit residues: 6.6289
Evaluate side-chains
  45 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 24
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  652 CYS
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0670
   chunk 120 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 136 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    1.7924

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.072597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.059642 restraints weight = 41778.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061198 restraints weight = 21816.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.062227 restraints weight = 13976.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.062919 restraints weight = 10310.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.063380 restraints weight = 8321.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11903  Z= 0.166
  Angle     :  0.542   9.120  16315  Z= 0.277
  Chirality :  0.041   0.141   1994
  Planarity :  0.004   0.038   1922
  Dihedral  : 12.427 154.988   2143
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.07 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.24), residues: 1337
  helix: -0.97 (0.54), residues: 106
  sheet: -2.66 (0.39), residues: 198
  loop : -1.35 (0.20), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 504 
 TYR   0.013   0.001   TYR A 469 
 PHE   0.011   0.001   PHE B 460 
 TRP   0.009   0.001   TRP B 547 
 HIS   0.003   0.001   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 (11895)
  covalent geometry    : angle       0.54203 /  0.28 (16299)
  SS BOND              : bond        0.00419 /  0.26 (    8)
  SS BOND              : angle       0.78699 /  0.38 (   16)
  hydrogen bonds       : bond        0.03547 /  2.22 (  100)
  hydrogen bonds       : angle       5.65940 /  3.95 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 28
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6211 (p90)
REVERT: A  512 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8565 (tt)
REVERT: B   24 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.3506 (t80)
REVERT: B  484 GLN cc_start: 0.8004 (tt0) cc_final: 0.7200 (tm-30)
  outliers start: 31
  outliers final: 18
  residues processed: 57
  average time/residue: 0.0698
  time to fit residues: 6.9967
Evaluate side-chains
  47 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 26
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.071212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.058297 restraints weight = 42943.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.059797 restraints weight = 22786.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.060796 restraints weight = 14765.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.061452 restraints weight = 10943.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.061863 restraints weight = 8919.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  11903  Z= 0.260
  Angle     :  0.638   7.591  16315  Z= 0.325
  Chirality :  0.044   0.174   1994
  Planarity :  0.004   0.038   1922
  Dihedral  : 12.874 149.708   2143
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.23 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.23), residues: 1337
  helix: -1.14 (0.51), residues: 112
  sheet: -2.87 (0.37), residues: 207
  loop : -1.48 (0.20), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 545 
 TYR   0.017   0.002   TYR A 469 
 PHE   0.016   0.001   PHE B 460 
 TRP   0.012   0.002   TRP B 547 
 HIS   0.004   0.001   HIS A 540 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00590 /  0.26 (11895)
  covalent geometry    : angle       0.63799 /  0.33 (16299)
  SS BOND              : bond        0.00545 /  0.31 (    8)
  SS BOND              : angle       0.94046 /  0.48 (   16)
  hydrogen bonds       : bond        0.04129 /  2.56 (  100)
  hydrogen bonds       : angle       5.97171 /  4.20 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 28
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6099 (p90)
REVERT: A  512 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8657 (tt)
REVERT: B   24 TYR cc_start: 0.4546 (OUTLIER) cc_final: 0.3767 (t80)
REVERT: B  484 GLN cc_start: 0.8188 (tt0) cc_final: 0.7196 (tm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 55
  average time/residue: 0.0635
  time to fit residues: 6.2627
Evaluate side-chains
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 26
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  650 CYS
Chi-restraints excluded: chain B residue  652 CYS
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 23 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 116 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 123 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 337 GLN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 585 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.072645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.059828 restraints weight = 41908.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.061368 restraints weight = 21975.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.062390 restraints weight = 14093.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.063059 restraints weight = 10372.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.063514 restraints weight = 8407.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11903  Z= 0.132
  Angle     :  0.533   8.231  16315  Z= 0.271
  Chirality :  0.040   0.182   1994
  Planarity :  0.004   0.038   1922
  Dihedral  : 12.667 152.923   2143
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.79 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.24), residues: 1337
  helix: -1.09 (0.52), residues: 112
  sheet: -2.56 (0.40), residues: 195
  loop : -1.37 (0.20), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.009   0.001   PHE B 460 
 TRP   0.012   0.001   TRP B 547 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 (11895)
  covalent geometry    : angle       0.53291 /  0.27 (16299)
  SS BOND              : bond        0.00371 /  0.22 (    8)
  SS BOND              : angle       0.80044 /  0.39 (   16)
  hydrogen bonds       : bond        0.03271 /  2.02 (  100)
  hydrogen bonds       : angle       5.65200 /  3.99 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 25
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.5734 (p90)
REVERT: A  512 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8561 (tt)
REVERT: A  539 GLN cc_start: 0.8913 (mp10) cc_final: 0.8543 (mp10)
REVERT: B   24 TYR cc_start: 0.4411 (OUTLIER) cc_final: 0.3470 (t80)
REVERT: B  484 GLN cc_start: 0.8114 (tt0) cc_final: 0.7194 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 50
  average time/residue: 0.0769
  time to fit residues: 6.6615
Evaluate side-chains
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 25
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  567 ILE
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 126 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 133 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.073426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.060538 restraints weight = 42245.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.062114 restraints weight = 21850.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.063170 restraints weight = 13903.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.063867 restraints weight = 10158.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.064314 restraints weight = 8179.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11903  Z= 0.095
  Angle     :  0.502   8.719  16315  Z= 0.252
  Chirality :  0.039   0.188   1994
  Planarity :  0.004   0.038   1922
  Dihedral  : 12.344 156.967   2143
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.63 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.24), residues: 1337
  helix: -1.03 (0.52), residues: 112
  sheet: -2.37 (0.40), residues: 200
  loop : -1.25 (0.20), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 326 
 TYR   0.012   0.001   TYR A 469 
 PHE   0.006   0.001   PHE A 687 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 (11895)
  covalent geometry    : angle       0.50135 /  0.25 (16299)
  SS BOND              : bond        0.00302 /  0.19 (    8)
  SS BOND              : angle       0.68338 /  0.34 (   16)
  hydrogen bonds       : bond        0.02873 /  1.75 (  100)
  hydrogen bonds       : angle       5.41586 /  3.80 (  240)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 24
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.5545 (p90)
REVERT: A  512 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8513 (tt)
REVERT: B   24 TYR cc_start: 0.4640 (OUTLIER) cc_final: 0.3654 (t80)
REVERT: B  484 GLN cc_start: 0.8042 (tt0) cc_final: 0.7092 (tm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 49
  average time/residue: 0.0752
  time to fit residues: 6.5526
Evaluate side-chains
  42 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 23
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 TYR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  650 CYS
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 120 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0070
   overall best weight:    1.2602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.073003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.060124 restraints weight = 42212.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.061695 restraints weight = 22031.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.062723 restraints weight = 14056.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.063403 restraints weight = 10338.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063800 restraints weight = 8350.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11903  Z= 0.120
  Angle     :  0.510   9.163  16315  Z= 0.256
  Chirality :  0.039   0.187   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 12.310 155.521   2143
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.87 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.24), residues: 1337
  helix: -0.85 (0.54), residues: 106
  sheet: -2.41 (0.41), residues: 193
  loop : -1.25 (0.20), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.012   0.001   TYR A 469 
 PHE   0.008   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 (11895)
  covalent geometry    : angle       0.50986 /  0.26 (16299)
  SS BOND              : bond        0.00311 /  0.19 (    8)
  SS BOND              : angle       0.68236 /  0.34 (   16)
  hydrogen bonds       : bond        0.03100 /  1.89 (  100)
  hydrogen bonds       : angle       5.47163 /  3.83 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1619.64 seconds
wall clock time: 28 minutes 52.28 seconds (1732.28 seconds total)