Starting phenix.real_space_refine
on Wed Mar  4 07:46:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7das_30626/03_2026/7das_30626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7das_30626/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7das_30626/03_2026/7das_30626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7das_30626/03_2026/7das_30626.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7das_30626/03_2026/7das_30626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7das_30626/03_2026/7das_30626.map"
  }
  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-5986/lib/python3.9/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: 690
          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: 2.37, per 1000 atoms: 0.20
  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: 0.98
  Conformation dependent library (CDL) restraints added in 564.3 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: 1.47
  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: 1.83

  Time building geometry restraints manager: 1.33 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: 7211
       33.25 -    66.49: 266
       66.49 -    99.74: 35
       99.74 -   132.99: 0
      132.99 -   166.23: 1
  Dihedral angle restraints: 7513
    sinusoidal: 3550
      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 7510 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:             5.480
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.480
  Find NCS groups from input model:        0.180
  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:1.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
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  : 16.890 166.233   4903
  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
  covalent geometry    : bond        0.00564 (11895)
  covalent geometry    : angle       0.91787 (16299)
  SS BOND              : bond        0.01190 (    8)
  SS BOND              : angle       1.62012 (   16)
  hydrogen bonds       : bond        0.23531 (  100)
  hydrogen bonds       : angle      10.52559 (  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  : 0.382 
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: 0.1465
  time to fit residues: 21.3249
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  : 0.431 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.074714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.061631 restraints weight = 40888.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.063180 restraints weight = 21304.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.064191 restraints weight = 13637.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.064863 restraints weight = 10064.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.065305 restraints weight = 8175.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  11903  Z= 0.245
  Angle     :  0.677  11.006  16315  Z= 0.348
  Chirality :  0.045   0.154   1994
  Planarity :  0.005   0.043   1922
  Dihedral  : 15.012 162.692   2245
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.82 %
    Favored  : 87.83 %
  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: -2.93 (0.22), residues: 1337
  helix: -1.29 (0.52), residues: 100
  sheet: -2.72 (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 453 
 HIS   0.005   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (11895)
  covalent geometry    : angle       0.67657 (16299)
  SS BOND              : bond        0.00545 (    8)
  SS BOND              : angle       1.12952 (   16)
  hydrogen bonds       : bond        0.04488 (  100)
  hydrogen bonds       : angle       6.58275 (  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
  50 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  538 PHE cc_start: 0.8559 (t80) cc_final: 0.8292 (t80)
REVERT: B   24 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4207 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 47
  average time/residue: 0.1017
  time to fit residues: 7.3889
Evaluate side-chains
  32 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  567 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.074817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.061466 restraints weight = 42037.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.063068 restraints weight = 21560.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.064150 restraints weight = 13688.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.064863 restraints weight = 9994.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.065340 restraints weight = 8064.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11903  Z= 0.145
  Angle     :  0.534   8.050  16315  Z= 0.276
  Chirality :  0.041   0.159   1994
  Planarity :  0.004   0.043   1922
  Dihedral  : 14.358 164.861   2245
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.29 %
    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: -2.46 (0.23), residues: 1337
  helix: -1.08 (0.55), residues: 100
  sheet: -2.62 (0.38), residues: 193
  loop : -1.61 (0.19), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 614 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.009   0.001   PHE B 460 
 TRP   0.011   0.001   TRP B 274 
 HIS   0.002   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11895)
  covalent geometry    : angle       0.53377 (16299)
  SS BOND              : bond        0.00665 (    8)
  SS BOND              : angle       0.87113 (   16)
  hydrogen bonds       : bond        0.03788 (  100)
  hydrogen bonds       : angle       5.92898 (  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
  51 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8555 (tt)
REVERT: B   24 TYR cc_start: 0.4491 (OUTLIER) cc_final: 0.3894 (t80)
REVERT: B  484 GLN cc_start: 0.7763 (tt0) cc_final: 0.7396 (mt0)
  outliers start: 17
  outliers final: 8
  residues processed: 50
  average time/residue: 0.0831
  time to fit residues: 7.0528
Evaluate side-chains
  36 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 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:    0.0770
   chunk 99 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0070
   chunk 11 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 GLN
B 682 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.076341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.063108 restraints weight = 40779.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.064809 restraints weight = 20416.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.065910 restraints weight = 12669.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.066657 restraints weight = 9126.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.067112 restraints weight = 7271.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11903  Z= 0.080
  Angle     :  0.500  12.016  16315  Z= 0.250
  Chirality :  0.038   0.176   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 13.883 164.128   2245
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.24 %
    Favored  : 84.65 %
  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: -2.09 (0.23), residues: 1337
  helix: -0.76 (0.59), residues: 94
  sheet: -2.53 (0.38), residues: 205
  loop : -1.27 (0.20), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 326 
 TYR   0.013   0.001   TYR A 469 
 PHE   0.008   0.001   PHE A 687 
 TRP   0.006   0.000   TRP B 274 
 HIS   0.014   0.001   HIS B 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 (11895)
  covalent geometry    : angle       0.49922 (16299)
  SS BOND              : bond        0.00349 (    8)
  SS BOND              : angle       0.73456 (   16)
  hydrogen bonds       : bond        0.02835 (  100)
  hydrogen bonds       : angle       5.56517 (  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
  54 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7091 (p90)
REVERT: A  512 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8465 (tt)
REVERT: B   24 TYR cc_start: 0.4437 (OUTLIER) cc_final: 0.3902 (t80)
REVERT: B   26 GLN cc_start: 0.8070 (mp10) cc_final: 0.7766 (mp10)
REVERT: B  484 GLN cc_start: 0.7631 (tt0) cc_final: 0.7289 (mt0)
  outliers start: 14
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0798
  time to fit residues: 6.9579
Evaluate side-chains
  35 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  347 ILE
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  459 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 99 optimal weight:    5.9990
   chunk 134 optimal weight:    9.9990
   chunk 118 optimal weight:    0.2980
   chunk 87 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  61 HIS
A 146 ASN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.072260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.059331 restraints weight = 42146.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.060809 restraints weight = 22713.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.061781 restraints weight = 14831.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.062442 restraints weight = 11073.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.062851 restraints weight = 9020.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  11903  Z= 0.262
  Angle     :  0.638   7.282  16315  Z= 0.328
  Chirality :  0.044   0.152   1994
  Planarity :  0.005   0.040   1922
  Dihedral  : 14.512 159.954   2245
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.12 %
    Favored  : 83.05 %
  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: -2.41 (0.23), residues: 1337
  helix: -1.24 (0.52), residues: 106
  sheet: -2.66 (0.39), residues: 189
  loop : -1.53 (0.20), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 457 
 TYR   0.016   0.002   TYR A 469 
 PHE   0.017   0.002   PHE B 460 
 TRP   0.014   0.002   TRP B 274 
 HIS   0.004   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (11895)
  covalent geometry    : angle       0.63806 (16299)
  SS BOND              : bond        0.00541 (    8)
  SS BOND              : angle       0.92822 (   16)
  hydrogen bonds       : bond        0.04253 (  100)
  hydrogen bonds       : angle       5.93068 (  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
  50 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 27
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7119 (p90)
REVERT: A  512 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8742 (tt)
REVERT: B   24 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3598 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 48
  average time/residue: 0.0760
  time to fit residues: 6.3135
Evaluate side-chains
  38 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 20
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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  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 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  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:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0070
   chunk 136 optimal weight:   20.0000
   chunk 138 optimal weight:   20.0000
   chunk 99 optimal weight:    3.9990
   overall best weight:    3.4006

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.071312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.058596 restraints weight = 42552.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.060035 restraints weight = 23082.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.060990 restraints weight = 15163.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.061637 restraints weight = 11318.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.062067 restraints weight = 9244.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040  11903  Z= 0.287
  Angle     :  0.654   6.945  16315  Z= 0.336
  Chirality :  0.045   0.195   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 15.062 155.604   2245
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.19 %
    Favored  : 82.42 %
  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: -2.53 (0.23), residues: 1337
  helix: -1.39 (0.49), residues: 112
  sheet: -2.81 (0.38), residues: 192
  loop : -1.59 (0.20), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 507 
 TYR   0.018   0.002   TYR A 469 
 PHE   0.018   0.002   PHE B 460 
 TRP   0.015   0.002   TRP B 274 
 HIS   0.005   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 (11895)
  covalent geometry    : angle       0.65375 (16299)
  SS BOND              : bond        0.00489 (    8)
  SS BOND              : angle       0.95327 (   16)
  hydrogen bonds       : bond        0.04422 (  100)
  hydrogen bonds       : angle       6.00661 (  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
  54 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 24
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6692 (p90)
REVERT: B   24 TYR cc_start: 0.4407 (OUTLIER) cc_final: 0.3697 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 52
  average time/residue: 0.0782
  time to fit residues: 6.9594
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  : 0.362 
-------------------------------------------------------------------------------
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  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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 76 optimal weight:    0.2980
   chunk 120 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 136 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 123 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3562 r_free = 0.3562 target = 0.073314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.060402 restraints weight = 41741.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.061989 restraints weight = 21691.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.063032 restraints weight = 13782.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.063720 restraints weight = 10070.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.064151 restraints weight = 8113.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11903  Z= 0.114
  Angle     :  0.514   8.218  16315  Z= 0.264
  Chirality :  0.039   0.154   1994
  Planarity :  0.004   0.039   1922
  Dihedral  : 14.759 155.930   2245
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.99 %
    Favored  : 82.10 %
  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: -2.22 (0.24), residues: 1337
  helix: -1.04 (0.53), residues: 106
  sheet: -2.64 (0.40), residues: 187
  loop : -1.38 (0.20), residues: 1044

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   0.008   0.001   PHE B 692 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (11895)
  covalent geometry    : angle       0.51281 (16299)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.17412 (   16)
  hydrogen bonds       : bond        0.03243 (  100)
  hydrogen bonds       : angle       5.71955 (  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
  53 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 29
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6182 (p90)
REVERT: A  512 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8514 (tt)
REVERT: A  539 GLN cc_start: 0.8848 (mp10) cc_final: 0.8626 (mp10)
REVERT: B   24 TYR cc_start: 0.4236 (OUTLIER) cc_final: 0.3608 (t80)
REVERT: B  484 GLN cc_start: 0.7960 (tt0) cc_final: 0.7117 (tm-30)
  outliers start: 24
  outliers final: 14
  residues processed: 51
  average time/residue: 0.0698
  time to fit residues: 6.2213
Evaluate side-chains
  42 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 25
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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  169 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3523 r_free = 0.3523 target = 0.071594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.058860 restraints weight = 42907.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.060306 restraints weight = 23278.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061258 restraints weight = 15299.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.061889 restraints weight = 11429.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.062293 restraints weight = 9401.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11903  Z= 0.238
  Angle     :  0.604   7.454  16315  Z= 0.310
  Chirality :  0.043   0.176   1994
  Planarity :  0.004   0.038   1922
  Dihedral  : 15.043 150.218   2245
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.15 %
    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: -2.40 (0.23), residues: 1337
  helix: -1.12 (0.51), residues: 112
  sheet: -2.87 (0.38), residues: 198
  loop : -1.47 (0.20), residues: 1027

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 545 
 TYR   0.016   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 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (11895)
  covalent geometry    : angle       0.60307 (16299)
  SS BOND              : bond        0.00680 (    8)
  SS BOND              : angle       1.01519 (   16)
  hydrogen bonds       : bond        0.04031 (  100)
  hydrogen bonds       : angle       5.92459 (  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
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 24
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6088 (p90)
REVERT: A  512 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8654 (tt)
REVERT: A  539 GLN cc_start: 0.8882 (mp10) cc_final: 0.8677 (mp10)
REVERT: B   24 TYR cc_start: 0.4323 (OUTLIER) cc_final: 0.3610 (t80)
REVERT: B  484 GLN cc_start: 0.8129 (tt0) cc_final: 0.7355 (tm-30)
  outliers start: 24
  outliers final: 16
  residues processed: 46
  average time/residue: 0.0769
  time to fit residues: 6.0969
Evaluate side-chains
  44 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 25
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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  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  169 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 116 optimal weight:    8.9990
   chunk 106 optimal weight:    4.9990
   chunk 123 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3529 r_free = 0.3529 target = 0.071976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.059184 restraints weight = 42310.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.060691 restraints weight = 22303.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.061700 restraints weight = 14382.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.062353 restraints weight = 10634.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.062803 restraints weight = 8659.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11903  Z= 0.202
  Angle     :  0.573   7.899  16315  Z= 0.295
  Chirality :  0.042   0.188   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 15.140 148.137   2245
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.71 %
    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: -2.33 (0.24), residues: 1337
  helix: -1.10 (0.51), residues: 112
  sheet: -2.77 (0.38), residues: 200
  loop : -1.42 (0.20), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 188 
 TYR   0.015   0.001   TYR A 469 
 PHE   0.012   0.001   PHE B 460 
 TRP   0.013   0.001   TRP B 547 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (11895)
  covalent geometry    : angle       0.57239 (16299)
  SS BOND              : bond        0.00524 (    8)
  SS BOND              : angle       0.97042 (   16)
  hydrogen bonds       : bond        0.03672 (  100)
  hydrogen bonds       : angle       5.79484 (  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
  49 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 26
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.5858 (p90)
REVERT: A  512 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (tt)
REVERT: A  539 GLN cc_start: 0.8919 (mp10) cc_final: 0.8596 (mp10)
REVERT: B   24 TYR cc_start: 0.4359 (OUTLIER) cc_final: 0.3419 (t80)
REVERT: B  484 GLN cc_start: 0.8177 (tt0) cc_final: 0.7216 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 47
  average time/residue: 0.0690
  time to fit residues: 5.7936
Evaluate side-chains
  46 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 24
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  185 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  578 ILE
Chi-restraints excluded: chain B residue  652 CYS
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:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 133 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3532 r_free = 0.3532 target = 0.072146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.059308 restraints weight = 42839.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.060829 restraints weight = 22445.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.061849 restraints weight = 14437.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.062502 restraints weight = 10648.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.062911 restraints weight = 8673.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.4758

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= 0.170
  Angle     :  0.548   8.080  16315  Z= 0.282
  Chirality :  0.041   0.182   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 15.036 149.413   2245
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.15 %
    Favored  : 81.62 %
  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: -2.25 (0.24), residues: 1337
  helix: -1.01 (0.51), residues: 112
  sheet: -2.76 (0.39), residues: 201
  loop : -1.36 (0.20), residues: 1024

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   0.012   0.001   PHE B 460 
 TRP   0.013   0.001   TRP B 547 
 HIS   0.002   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (11895)
  covalent geometry    : angle       0.54746 (16299)
  SS BOND              : bond        0.00419 (    8)
  SS BOND              : angle       0.86166 (   16)
  hydrogen bonds       : bond        0.03554 (  100)
  hydrogen bonds       : angle       5.69064 (  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
  54 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 26
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.5781 (p90)
REVERT: A  512 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8584 (tt)
REVERT: A  539 GLN cc_start: 0.8893 (mp10) cc_final: 0.8610 (mp10)
REVERT: B   24 TYR cc_start: 0.4500 (OUTLIER) cc_final: 0.3514 (t80)
REVERT: B   81 LEU cc_start: 0.8242 (mp) cc_final: 0.8039 (tt)
REVERT: B  118 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8056 (pp30)
REVERT: B  484 GLN cc_start: 0.8157 (tt0) cc_final: 0.7244 (tm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 53
  average time/residue: 0.0758
  time to fit residues: 7.0378
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  : 0.469 
-------------------------------------------------------------------------------
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  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  347 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 120 optimal weight:    0.0770
   chunk 22 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 128 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    1.6942

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3533 r_free = 0.3533 target = 0.072193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.059386 restraints weight = 42641.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060920 restraints weight = 22284.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.061933 restraints weight = 14298.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.062604 restraints weight = 10516.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.063009 restraints weight = 8526.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.4840

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= 0.153
  Angle     :  0.535   8.381  16315  Z= 0.275
  Chirality :  0.040   0.182   1994
  Planarity :  0.004   0.040   1922
  Dihedral  : 14.997 151.165   2245
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.71 %
    Favored  : 81.54 %
  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: -1.17 (0.50), residues: 118
  sheet: -2.66 (0.39), residues: 204
  loop : -1.31 (0.20), residues: 1015

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   0.010   0.001   PHE B 460 
 TRP   0.013   0.001   TRP A 547 
 HIS   0.002   0.000   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11895)
  covalent geometry    : angle       0.53437 (16299)
  SS BOND              : bond        0.00388 (    8)
  SS BOND              : angle       0.83394 (   16)
  hydrogen bonds       : bond        0.03380 (  100)
  hydrogen bonds       : angle       5.66697 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1715.80 seconds
wall clock time: 30 minutes 35.65 seconds (1835.65 seconds total)