Starting phenix.real_space_refine
on Fri Sep 11 22:18:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7das_30626/09_2026/7das_30626.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11603
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5418
          Classifications: {'peptide': 674}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 645}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 671, 5393
          Classifications: {'peptide': 671}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 792
          Classifications: {'RNAv2': 66}
          Modifications used: {'rna3p_pur': 32, 'rna3p_pyr': 34}
          Link IDs: {'rna3p': 65}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 707
          Unresolved non-hydrogen angles: 1118
          Unresolved non-hydrogen dihedrals: 492
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'  U%rna3p_pyr:plan': 12, '  G%rna3p_pur:plan': 17, '  G%rna3p_pur:plan2': 17, '  A%rna3p_pur:plan': 15, '  A%rna3p_pur:plan2': 15, '  C%rna3p_pyr:plan': 22, '  C%rna3p_pyr:plan2': 22}
          Unresolved non-hydrogen planarities: 717
  Time building chain proxies: 2.72, per 1000 atoms: 0.23
  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: 0.96
  Conformation dependent library (CDL) restraints added in 493.6 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: 1.19
  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: 1.98

  Time building geometry restraints manager: 1.29 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=" O3'   G C  10 "
       pdb=" P     A C  11 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.20e-02 6.94e+03 2.20e+01
  bond pdb=" O3'   A C  34 "
       pdb=" P     C C  35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.20e-02 6.94e+03 2.18e+01
  bond pdb=" O3'   G C  13 "
       pdb=" P     G C  14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.20e-02 6.94e+03 2.07e+01
  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
  ... (remaining 11890 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 15643
        2.30 -     4.59: 578
        4.59 -     6.89: 63
        6.89 -     9.19: 9
        9.19 -    11.49: 6
  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
     113.80  125.15  -11.35 2.00e+00 2.50e-01 3.22e+01
  angle pdb=" C3'   G C  18 "
        pdb=" C2'   G C  18 "
        pdb=" O2'   G C  18 "
      ideal   model   delta    sigma   weight residual
     109.80  120.23  -10.43 2.00e+00 2.50e-01 2.72e+01
  angle pdb=" N   VAL A 491 "
        pdb=" CA  VAL A 491 "
        pdb=" C   VAL A 491 "
      ideal   model   delta    sigma   weight residual
     113.10  108.12    4.98 9.70e-01 1.06e+00 2.63e+01
  ... (remaining 16294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 7151
       33.25 -    66.49: 237
       66.49 -    99.74: 22
       99.74 -   132.99: 0
      132.99 -   166.23: 1
  Dihedral angle restraints: 7411
    sinusoidal: 3448
      harmonic: 3963
  Sorted by residual:
  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
      36.34  -40.89   77.24     1      3.10e+00 1.04e-01 7.78e+02
  dihedral pdb=" C4'   C C  42 "
           pdb=" C3'   C C  42 "
           pdb=" C2'   C C  42 "
           pdb=" C1'   C C  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -36.89   73.24     1      3.10e+00 1.04e-01 7.11e+02
  dihedral pdb=" C4'   A C  25 "
           pdb=" C3'   A C  25 "
           pdb=" C2'   A C  25 "
           pdb=" C1'   A C  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -20.24   56.58     1      3.10e+00 1.04e-01 4.49e+02
  ... (remaining 7408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.182: 1858
       0.182 -    0.363: 131
       0.363 -    0.545: 2
       0.545 -    0.726: 1
       0.726 -    0.908: 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     -2.50   -1.59   -0.91 2.00e-01 2.50e+01 2.06e+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     -2.50   -1.69   -0.81 2.00e-01 2.50e+01 1.62e+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     -2.79   -2.08   -0.71 2.00e-01 2.50e+01 1.27e+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:             3.930
  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:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     12.540
  Find NCS groups from input model:        0.190
  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:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  11903  Z= 0.343
  Angle     :  0.963  11.487  16315  Z= 0.564
  Chirality :  0.084   0.908   1994
  Planarity :  0.005   0.052   1922
  Dihedral  : 15.893 166.233   4801
  Min Nonbonded Distance : 1.496

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

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

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00560 /  0.34 (11895)
  covalent geometry    : angle       0.96239 /  0.56 (16299)
  SS BOND              : bond        0.01190 /  0.62 (    8)
  SS BOND              : angle       1.62012 /  0.82 (   16)
  hydrogen bonds       : bond        0.23531 / 14.87 (  100)
  hydrogen bonds       : angle      10.52559 /  6.89 (  240)

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

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.440 
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: 0.1435
  time to fit residues: 21.2795
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  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.6986

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

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.074827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.061739 restraints weight = 40924.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063289 restraints weight = 21278.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.064291 restraints weight = 13625.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.064912 restraints weight = 10028.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.065384 restraints weight = 8222.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  11903  Z= 0.248
  Angle     :  0.740  11.316  16315  Z= 0.359
  Chirality :  0.048   0.274   1994
  Planarity :  0.005   0.043   1922
  Dihedral  : 10.245 166.301   2143
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.74 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.22), residues: 1337
  helix: -1.33 (0.52), residues: 100
  sheet: -2.76 (0.37), residues: 175
  loop : -2.04 (0.18), residues: 1062

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   0.006   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00566 /  0.25 (11895)
  covalent geometry    : angle       0.73906 /  0.36 (16299)
  SS BOND              : bond        0.00649 /  0.36 (    8)
  SS BOND              : angle       1.17612 /  0.57 (   16)
  hydrogen bonds       : bond        0.04407 /  2.71 (  100)
  hydrogen bonds       : angle       6.61380 /  4.45 (  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
  51 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  538 PHE cc_start: 0.8554 (t80) cc_final: 0.8291 (t80)
REVERT: B   24 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.4142 (t80)
  outliers start: 17
  outliers final: 8
  residues processed: 48
  average time/residue: 0.1028
  time to fit residues: 7.7790
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  : 0.451 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0020
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.4388

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.076479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.063096 restraints weight = 40884.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.064782 restraints weight = 20508.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.065888 restraints weight = 12820.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.066623 restraints weight = 9266.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.067069 restraints weight = 7417.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11903  Z= 0.088
  Angle     :  0.551   8.177  16315  Z= 0.271
  Chirality :  0.043   0.226   1994
  Planarity :  0.004   0.040   1922
  Dihedral  :  9.289 166.532   2143
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.41 %
    Favored  : 86.56 %
  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: -2.30 (0.23), residues: 1337
  helix: -0.71 (0.60), residues: 88
  sheet: -2.63 (0.37), residues: 198
  loop : -1.47 (0.19), residues: 1051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 326 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.007   0.001   PHE A 687 
 TRP   0.008   0.001   TRP B 547 
 HIS   0.001   0.000   HIS A 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00195 /  0.09 (11895)
  covalent geometry    : angle       0.55087 /  0.27 (16299)
  SS BOND              : bond        0.00369 /  0.25 (    8)
  SS BOND              : angle       0.78571 /  0.39 (   16)
  hydrogen bonds       : bond        0.03240 /  1.99 (  100)
  hydrogen bonds       : angle       5.87944 /  4.02 (  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
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8521 (tt)
REVERT: B   24 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.4072 (t80)
REVERT: B  484 GLN cc_start: 0.7645 (tt0) cc_final: 0.7310 (mt0)
  outliers start: 13
  outliers final: 3
  residues processed: 51
  average time/residue: 0.0849
  time to fit residues: 7.3743
Evaluate side-chains
  31 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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 B residue   24 TYR
Chi-restraints excluded: chain B residue  347 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 99 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 HIS
A 146 ASN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS
B 146 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.072971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.059581 restraints weight = 42153.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.061124 restraints weight = 22005.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.062182 restraints weight = 14128.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.062876 restraints weight = 10363.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.063345 restraints weight = 8392.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  11903  Z= 0.242
  Angle     :  0.670  10.564  16315  Z= 0.328
  Chirality :  0.047   0.260   1994
  Planarity :  0.004   0.040   1922
  Dihedral  :  9.332 163.821   2143
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.92 %
    Favored  : 84.17 %
  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: -1.07 (0.54), residues: 100
  sheet: -2.59 (0.39), residues: 189
  loop : -1.57 (0.19), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 507 
 TYR   0.015   0.002   TYR A 469 
 PHE   0.016   0.002   PHE B 460 
 TRP   0.012   0.002   TRP B 274 
 HIS   0.004   0.001   HIS A 540 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.24 (11895)
  covalent geometry    : angle       0.66931 /  0.33 (16299)
  SS BOND              : bond        0.00868 /  0.59 (    8)
  SS BOND              : angle       0.92100 /  0.47 (   16)
  hydrogen bonds       : bond        0.04169 /  2.55 (  100)
  hydrogen bonds       : angle       5.99067 /  4.09 (  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
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 28
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7308 (p90)
REVERT: A  512 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8697 (tt)
REVERT: B   24 TYR cc_start: 0.4468 (OUTLIER) cc_final: 0.3833 (t80)
  outliers start: 24
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0784
  time to fit residues: 6.7638
Evaluate side-chains
  38 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 134 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.9582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.074859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.061485 restraints weight = 42049.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.063219 restraints weight = 20731.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.064349 restraints weight = 12779.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.065090 restraints weight = 9164.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.065542 restraints weight = 7308.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11903  Z= 0.106
  Angle     :  0.553   9.061  16315  Z= 0.270
  Chirality :  0.043   0.232   1994
  Planarity :  0.004   0.039   1922
  Dihedral  :  8.860 167.167   2143
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.72 %
    Favored  : 83.69 %
  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 (0.23), residues: 1337
  helix: -1.04 (0.55), residues: 100
  sheet: -2.58 (0.39), residues: 194
  loop : -1.38 (0.20), residues: 1043

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.013   0.001   TYR A 469 
 PHE   0.007   0.001   PHE A 687 
 TRP   0.008   0.001   TRP B 274 
 HIS   0.002   0.000   HIS A 682 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 (11895)
  covalent geometry    : angle       0.55251 /  0.27 (16299)
  SS BOND              : bond        0.00268 /  0.15 (    8)
  SS BOND              : angle       0.77588 /  0.37 (   16)
  hydrogen bonds       : bond        0.03200 /  1.96 (  100)
  hydrogen bonds       : angle       5.60676 /  3.86 (  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
  47 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 27
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7059 (p90)
REVERT: A  512 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (tt)
REVERT: B   24 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.3760 (t80)
REVERT: B  484 GLN cc_start: 0.7826 (tt0) cc_final: 0.7182 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 44
  average time/residue: 0.0910
  time to fit residues: 6.9164
Evaluate side-chains
  43 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 26
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  522 ILE
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   75 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  567 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 129 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 136 optimal weight:    8.9990
   chunk 138 optimal weight:    9.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    2.7186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.072311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.059333 restraints weight = 41970.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.060871 restraints weight = 21902.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.061892 restraints weight = 14016.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.062570 restraints weight = 10301.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.062985 restraints weight = 8334.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033  11903  Z= 0.245
  Angle     :  0.662   8.452  16315  Z= 0.326
  Chirality :  0.047   0.221   1994
  Planarity :  0.004   0.039   1922
  Dihedral  :  9.161 160.961   2143
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.96 %
    Favored  : 82.82 %
  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: -1.32 (0.50), residues: 112
  sheet: -2.85 (0.37), residues: 200
  loop : -1.45 (0.20), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 507 
 TYR   0.016   0.002   TYR A 469 
 PHE   0.016   0.001   PHE B 460 
 TRP   0.014   0.002   TRP B 274 
 HIS   0.004   0.001   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.25 (11895)
  covalent geometry    : angle       0.66214 /  0.33 (16299)
  SS BOND              : bond        0.00421 /  0.22 (    8)
  SS BOND              : angle       0.94675 /  0.49 (   16)
  hydrogen bonds       : bond        0.04105 /  2.50 (  100)
  hydrogen bonds       : angle       5.93966 /  4.08 (  240)

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

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 28
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6865 (p90)
REVERT: A  512 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8663 (tt)
REVERT: B   24 TYR cc_start: 0.4457 (OUTLIER) cc_final: 0.3680 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 54
  average time/residue: 0.0743
  time to fit residues: 7.0102
Evaluate side-chains
  43 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 22
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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  496 VAL
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 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:    4.9990
   chunk 129 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 120 optimal weight:    0.4980
   chunk 107 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 128 optimal weight:    4.9990
   chunk 136 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 123 optimal weight:    5.9990
   overall best weight:    1.8984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.072893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.059934 restraints weight = 41802.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.061505 restraints weight = 21774.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.062534 restraints weight = 13899.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.063218 restraints weight = 10196.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.063673 restraints weight = 8252.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11903  Z= 0.169
  Angle     :  0.591   8.670  16315  Z= 0.290
  Chirality :  0.045   0.214   1994
  Planarity :  0.004   0.038   1922
  Dihedral  :  8.974 157.346   2143
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  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: -2.27 (0.23), residues: 1337
  helix: -1.03 (0.53), residues: 106
  sheet: -2.83 (0.38), residues: 198
  loop : -1.36 (0.20), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 504 
 TYR   0.015   0.001   TYR A 469 
 PHE   0.011   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.001   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 (11895)
  covalent geometry    : angle       0.59031 /  0.29 (16299)
  SS BOND              : bond        0.00347 /  0.19 (    8)
  SS BOND              : angle       0.83805 /  0.42 (   16)
  hydrogen bonds       : bond        0.03623 /  2.25 (  100)
  hydrogen bonds       : angle       5.76717 /  4.00 (  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
  48 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 24
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6486 (p90)
REVERT: A  512 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (tt)
REVERT: B   24 TYR cc_start: 0.4489 (OUTLIER) cc_final: 0.3714 (t80)
REVERT: B  484 GLN cc_start: 0.7990 (tt0) cc_final: 0.7183 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 46
  average time/residue: 0.0715
  time to fit residues: 5.9906
Evaluate side-chains
  43 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 22
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
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  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  522 ILE
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 78 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    1.3784

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.073499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.060532 restraints weight = 42429.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.062130 restraints weight = 22091.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.063182 restraints weight = 14017.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.063882 restraints weight = 10278.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.064352 restraints weight = 8276.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4195

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= 0.133
  Angle     :  0.558   8.618  16315  Z= 0.274
  Chirality :  0.043   0.200   1994
  Planarity :  0.004   0.038   1922
  Dihedral  :  8.617 155.269   2143
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.75 %
    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: -2.14 (0.24), residues: 1337
  helix: -0.95 (0.53), residues: 106
  sheet: -2.65 (0.40), residues: 187
  loop : -1.31 (0.20), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 326 
 TYR   0.012   0.001   TYR A 469 
 PHE   0.009   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 (11895)
  covalent geometry    : angle       0.55763 /  0.27 (16299)
  SS BOND              : bond        0.00405 /  0.26 (    8)
  SS BOND              : angle       0.74681 /  0.37 (   16)
  hydrogen bonds       : bond        0.03273 /  2.02 (  100)
  hydrogen bonds       : angle       5.55511 /  3.85 (  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
  53 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 26
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.5985 (p90)
REVERT: B   24 TYR cc_start: 0.4414 (OUTLIER) cc_final: 0.3677 (t80)
REVERT: B  484 GLN cc_start: 0.7959 (tt0) cc_final: 0.7172 (tm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 50
  average time/residue: 0.0754
  time to fit residues: 6.7353
Evaluate side-chains
  44 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 23
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  496 VAL
Chi-restraints excluded: chain A residue  522 ILE
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 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  652 CYS
Chi-restraints excluded: chain B residue  697 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.9184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.059721 restraints weight = 42081.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.061263 restraints weight = 22084.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.062286 restraints weight = 14179.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.062947 restraints weight = 10454.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.063396 restraints weight = 8493.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4333

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= 0.174
  Angle     :  0.595   8.253  16315  Z= 0.291
  Chirality :  0.045   0.197   1994
  Planarity :  0.004   0.039   1922
  Dihedral  :  8.694 153.084   2143
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.23 %
    Favored  : 81.78 %
  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: -2.18 (0.24), residues: 1337
  helix: -1.09 (0.52), residues: 112
  sheet: -2.73 (0.38), residues: 205
  loop : -1.27 (0.20), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 545 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.012   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.003   0.001   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.17 (11895)
  covalent geometry    : angle       0.59475 /  0.29 (16299)
  SS BOND              : bond        0.00448 /  0.28 (    8)
  SS BOND              : angle       0.78672 /  0.40 (   16)
  hydrogen bonds       : bond        0.03608 /  2.20 (  100)
  hydrogen bonds       : angle       5.73791 /  3.99 (  240)

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

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 27
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6013 (p90)
REVERT: A  512 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8607 (tt)
REVERT: B   24 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.3507 (t80)
REVERT: B  484 GLN cc_start: 0.8051 (tt0) cc_final: 0.7162 (tm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 50
  average time/residue: 0.0783
  time to fit residues: 6.9656
Evaluate side-chains
  49 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 25
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
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  522 ILE
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 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  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  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:    6.9990
   chunk 112 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 133 optimal weight:    0.3980
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.1782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.073619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.060664 restraints weight = 42497.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.062258 restraints weight = 21932.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.063300 restraints weight = 13919.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.063996 restraints weight = 10204.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.064417 restraints weight = 8240.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4415

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= 0.118
  Angle     :  0.554   8.272  16315  Z= 0.269
  Chirality :  0.043   0.202   1994
  Planarity :  0.004   0.038   1922
  Dihedral  :  8.530 154.483   2143
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.63 %
    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: -2.07 (0.24), residues: 1337
  helix: -1.09 (0.52), residues: 112
  sheet: -2.62 (0.39), residues: 205
  loop : -1.19 (0.21), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.013   0.001   TYR A 469 
 PHE   0.007   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 547 
 HIS   0.002   0.000   HIS B 682 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (11895)
  covalent geometry    : angle       0.55384 /  0.27 (16299)
  SS BOND              : bond        0.00381 /  0.25 (    8)
  SS BOND              : angle       0.71516 /  0.36 (   16)
  hydrogen bonds       : bond        0.03099 /  1.89 (  100)
  hydrogen bonds       : angle       5.55339 /  3.85 (  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
  47 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 25
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.5823 (p90)
REVERT: A  512 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: B   24 TYR cc_start: 0.4632 (OUTLIER) cc_final: 0.3605 (t80)
REVERT: B  484 GLN cc_start: 0.8035 (tt0) cc_final: 0.7132 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 46
  average time/residue: 0.0746
  time to fit residues: 6.1637
Evaluate side-chains
  43 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 22
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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  496 VAL
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  522 ILE
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  347 ILE
Chi-restraints excluded: chain B residue  565 LEU
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:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 128 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 108 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.9386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.072574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.059600 restraints weight = 42834.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061146 restraints weight = 22403.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.062176 restraints weight = 14367.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.062852 restraints weight = 10577.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.063208 restraints weight = 8590.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11903  Z= 0.175
  Angle     :  0.596   8.852  16315  Z= 0.291
  Chirality :  0.045   0.196   1994
  Planarity :  0.004   0.039   1922
  Dihedral  :  8.664 151.450   2143
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.63 %
    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: -2.17 (0.24), residues: 1337
  helix: -1.22 (0.50), residues: 118
  sheet: -2.69 (0.39), residues: 205
  loop : -1.26 (0.21), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 504 
 TYR   0.014   0.001   TYR A 469 
 PHE   0.012   0.001   PHE B 460 
 TRP   0.012   0.001   TRP B 547 
 HIS   0.003   0.001   HIS A 666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.18 (11895)
  covalent geometry    : angle       0.59605 /  0.29 (16299)
  SS BOND              : bond        0.00404 /  0.24 (    8)
  SS BOND              : angle       0.76193 /  0.38 (   16)
  hydrogen bonds       : bond        0.03640 /  2.24 (  100)
  hydrogen bonds       : angle       5.75083 /  4.00 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1835.27 seconds
wall clock time: 32 minutes 47.10 seconds (1967.10 seconds total)