Starting phenix.real_space_refine
on Tue Feb  3 20:37:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kve_62591/02_2026/9kve_62591.map"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4277      2.51       5
     N    1115      2.21       5
     O    1307      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6728
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 982
          Classifications: {'peptide': 128}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 793
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 925
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "G"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 802
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "C"
      Number of atoms: 1516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1516
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 874
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "F"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 836
          Classifications: {'peptide': 113}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 9, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 26
  Time building chain proxies: 1.63, per 1000 atoms: 0.24
  Number of scatterers: 6728
  At special positions: 0
  Unit cell: (73.45, 112.45, 107.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1307      8.00
     N    1115      7.00
     C    4277      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  94 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 269.2 milliseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1614

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 21 sheets defined
      5.0% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.507A  pdb=" N   SER A  31 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'E' and resid 28 through 30
      No H-bonds generated for 'chain 'E' and resid 28 through 30'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.799A  pdb=" N   THR E  91 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.919A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 3.865A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.528A  pdb=" N   TYR D  32 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.520A  pdb=" N   VAL A 122 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   MET A  34 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   VAL A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA A  40 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   GLY A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 12
      removed outlier: 6.310A  pdb=" N   VAL B  10 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 23
      removed outlier: 3.897A  pdb=" N   SER B  71 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 93
    Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.018A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 120 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   MET E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   VAL E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.018A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 120 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL E 100 " --> pdb=" O   MET E 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 4 through 6
    Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12
      removed outlier: 6.560A  pdb=" N   TRP G  35 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12
      removed outlier: 3.803A  pdb=" N   GLN G  90 " --> pdb=" O   THR G  97 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR G  97 " --> pdb=" O   GLN G  90 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 19 through 21
    Processing sheet with id=AB4, first strand: chain 'C' and resid 357 through 358
      removed outlier: 3.504A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.249A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL C 524 " --> pdb=" O   PHE C 392 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   PHE C 392 " --> pdb=" O   VAL C 524 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB9, first strand: chain 'D' and resid 58 through 60
      removed outlier: 5.212A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 100 through 101
      removed outlier: 3.589A  pdb=" N   ALA D 107 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 6
      removed outlier: 3.540A  pdb=" N   ASP F  76 " --> pdb=" O   SER F  73 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13
      removed outlier: 3.948A  pdb=" N   GLY F  90 " --> pdb=" O   VAL F 110 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU F  39 " --> pdb=" O   TYR F  55 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   TYR F  55 " --> pdb=" O   LEU F  39 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TRP F  41 " --> pdb=" O   LEU F  53 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    537 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: 1.02

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2147
        1.34 -     1.46: 1743
        1.46 -     1.58: 2973
        1.58 -     1.70: 0
        1.70 -     1.81: 38
  Bond restraints: 6901
  Sorted by residual:
  bond pdb=" C   THR F   7 "
       pdb=" N   PRO F   8 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 8.70e-03 1.32e+04 2.22e+00
  bond pdb=" CB  VAL C 401 "
       pdb=" CG1 VAL C 401 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  bond pdb=" CB  ASN A  52 "
       pdb=" CG  ASN A  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.492  0.024 2.50e-02 1.60e+03 9.40e-01
  bond pdb=" N   TYR D 109 "
       pdb=" CA  TYR D 109 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.012 1.29e-02 6.01e+03 9.15e-01
  bond pdb=" CB  VAL F  57 "
       pdb=" CG1 VAL F  57 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.00e-01
  ... (remaining 6896 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 8958
        1.52 -     3.03: 395
        3.03 -     4.55: 51
        4.55 -     6.06: 7
        6.06 -     7.58: 4
  Bond angle restraints: 9415
  Sorted by residual:
  angle pdb=" CA  TYR G  94 "
        pdb=" CB  TYR G  94 "
        pdb=" CG  TYR G  94 "
      ideal   model   delta    sigma   weight residual
     113.90  106.68    7.22 1.80e+00 3.09e-01 1.61e+01
  angle pdb=" C   ASN A  52 "
        pdb=" CA  ASN A  52 "
        pdb=" CB  ASN A  52 "
      ideal   model   delta    sigma   weight residual
     112.99  106.98    6.01 2.10e+00 2.27e-01 8.20e+00
  angle pdb=" CA  GLY D 111 "
        pdb=" C   GLY D 111 "
        pdb=" N   GLN D 112 "
      ideal   model   delta    sigma   weight residual
     114.30  117.67   -3.37 1.20e+00 6.94e-01 7.89e+00
  angle pdb=" N   TYR G  94 "
        pdb=" CA  TYR G  94 "
        pdb=" C   TYR G  94 "
      ideal   model   delta    sigma   weight residual
     109.81  115.92   -6.11 2.21e+00 2.05e-01 7.64e+00
  angle pdb=" C   SER B  64 "
        pdb=" N   GLY B  65 "
        pdb=" CA  GLY B  65 "
      ideal   model   delta    sigma   weight residual
     122.33  120.32    2.01 7.30e-01 1.88e+00 7.56e+00
  ... (remaining 9410 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 3656
       17.02 -    34.03: 296
       34.03 -    51.05: 40
       51.05 -    68.06: 8
       68.06 -    85.08: 5
  Dihedral angle restraints: 4005
    sinusoidal: 1450
      harmonic: 2555
  Sorted by residual:
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.46   50.46     1      1.00e+01 1.00e-02 3.49e+01
  dihedral pdb=" CA  ASN G  93 "
           pdb=" C   ASN G  93 "
           pdb=" N   TYR G  94 "
           pdb=" CA  TYR G  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.91  -27.09     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  TYR A 110 "
           pdb=" C   TYR A 110 "
           pdb=" N   THR A 111 "
           pdb=" CA  THR A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.35  -26.65     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 4002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 771
       0.046 -    0.091: 187
       0.091 -    0.137: 67
       0.137 -    0.183: 8
       0.183 -    0.228: 1
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  TYR G  94 "
            pdb=" N   TYR G  94 "
            pdb=" C   TYR G  94 "
            pdb=" CB  TYR G  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  ILE F  54 "
            pdb=" N   ILE F  54 "
            pdb=" C   ILE F  54 "
            pdb=" CB  ILE F  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1217
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  94 "   -0.022 2.00e-02 2.50e+03   1.57e-02 4.93e+00
        pdb=" CG  TYR G  94 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  94 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR G  94 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G   7 "   -0.036 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO G   8 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO G   8 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO G   8 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  13 "   -0.034 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO D  14 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO D  14 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D  14 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1214 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 83
        2.65 -     3.21: 5860
        3.21 -     3.77: 9582
        3.77 -     4.34: 14607
        4.34 -     4.90: 24875
  Nonbonded interactions: 55007
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 359 "
            pdb=" OD1 ASN C 394 "
     model   vdw
     2.084 3.040
  nonbonded pdb=" O   SER A  30 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   PRO F   8 "
            pdb=" OG1 THR F 108 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER A 114 "
            pdb=" ND2 ASN B  35 "
     model   vdw
     2.242 3.120
  ... (remaining 55002 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.960
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
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      :  0.004   0.034   6911  Z= 0.200
  Angle     :  0.733   7.576   9435  Z= 0.425
  Chirality :  0.046   0.228   1034
  Planarity :  0.005   0.053   1217
  Dihedral  : 12.696  85.077   2361
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.36 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.80 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.25), residues: 880
  helix: -4.98 (0.28), residues: 19
  sheet: -1.44 (0.25), residues: 380
  loop : -2.40 (0.24), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 108 
 TYR   0.038   0.002   TYR G  94 
 PHE   0.032   0.002   PHE C 347 
 TRP   0.012   0.001   TRP D  33 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 6901)
  covalent geometry    : angle       0.73247 ( 9415)
  SS BOND              : bond        0.00475 (   10)
  SS BOND              : angle       0.97914 (   20)
  hydrogen bonds       : bond        0.13203 (  214)
  hydrogen bonds       : angle       7.76561 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLN cc_start: 0.7166 (tt0) cc_final: 0.6690 (pt0)
REVERT: B   64 SER cc_start: 0.7618 (m) cc_final: 0.7287 (p)
REVERT: E   32 TYR cc_start: 0.7200 (m-80) cc_final: 0.6980 (m-80)
REVERT: E   60 TYR cc_start: 0.7615 (m-80) cc_final: 0.6705 (m-80)
REVERT: G   32 TYR cc_start: 0.7409 (m-80) cc_final: 0.7184 (m-80)
REVERT: G   55 GLU cc_start: 0.7060 (tp30) cc_final: 0.6850 (mm-30)
REVERT: G   91 TYR cc_start: 0.6756 (p90) cc_final: 0.6430 (p90)
REVERT: C  453 TYR cc_start: 0.7863 (p90) cc_final: 0.7506 (p90)
REVERT: C  515 PHE cc_start: 0.7928 (m-80) cc_final: 0.7598 (m-80)
REVERT: C  516 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6261 (mt-10)
REVERT: C  523 THR cc_start: 0.7571 (p) cc_final: 0.7352 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 137
  average time/residue: 0.3862
  time to fit residues: 56.9079
Evaluate side-chains
  130 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0040
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.3150

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
B  35 ASN
E  84 ASN
** E 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 343 ASN
C 354 ASN
C 360 ASN
C 370 ASN
C 422 ASN
C 439 ASN
D  39 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124998 restraints weight = 9683.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.10
r_work: 0.3526 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6911  Z= 0.122
  Angle     :  0.605  10.991   9435  Z= 0.315
  Chirality :  0.045   0.216   1034
  Planarity :  0.005   0.049   1217
  Dihedral  :  5.453  38.453    978
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 10.27 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.27), residues: 880
  helix: -4.28 (0.55), residues: 19
  sheet: -0.74 (0.26), residues: 377
  loop : -1.61 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 100 
 TYR   0.030   0.002   TYR G  94 
 PHE   0.018   0.001   PHE F  93 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.005   0.002   HIS E 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6901)
  covalent geometry    : angle       0.60522 ( 9415)
  SS BOND              : bond        0.00389 (   10)
  SS BOND              : angle       0.66686 (   20)
  hydrogen bonds       : bond        0.03322 (  214)
  hydrogen bonds       : angle       5.83962 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 TRP cc_start: 0.8303 (m100) cc_final: 0.7606 (m100)
REVERT: B   37 TYR cc_start: 0.8256 (m-80) cc_final: 0.7992 (m-80)
REVERT: B   38 GLN cc_start: 0.7541 (tt0) cc_final: 0.7016 (pt0)
REVERT: B   51 ASP cc_start: 0.8030 (m-30) cc_final: 0.7702 (m-30)
REVERT: B   64 SER cc_start: 0.7954 (m) cc_final: 0.7737 (p)
REVERT: E   32 TYR cc_start: 0.7543 (m-80) cc_final: 0.7303 (m-80)
REVERT: E   60 TYR cc_start: 0.8005 (m-80) cc_final: 0.7033 (m-80)
  outliers start: 19
  outliers final: 8
  residues processed: 135
  average time/residue: 0.3584
  time to fit residues: 52.2361
Evaluate side-chains
  130 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain G residue   73 LEU
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain F residue   49 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
B  54 ASN
G  92 ASN
C 498 GLN
C 501 ASN
D  39 GLN
F  44 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.139956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.125977 restraints weight = 9337.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.96
r_work: 0.3522 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6911  Z= 0.231
  Angle     :  0.689  12.565   9435  Z= 0.364
  Chirality :  0.047   0.185   1034
  Planarity :  0.005   0.048   1217
  Dihedral  :  5.863  33.280    978
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.10 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.27), residues: 880
  helix: -4.33 (0.38), residues: 26
  sheet: -0.34 (0.26), residues: 397
  loop : -1.43 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 357 
 TYR   0.029   0.003   TYR F  55 
 PHE   0.021   0.002   PHE D  37 
 TRP   0.017   0.003   TRP A  47 
 HIS   0.007   0.002   HIS E 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 6901)
  covalent geometry    : angle       0.68875 ( 9415)
  SS BOND              : bond        0.00592 (   10)
  SS BOND              : angle       0.80101 (   20)
  hydrogen bonds       : bond        0.03893 (  214)
  hydrogen bonds       : angle       5.95928 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLN cc_start: 0.7579 (tt0) cc_final: 0.6983 (pt0)
REVERT: B   51 ASP cc_start: 0.8052 (m-30) cc_final: 0.7650 (m-30)
REVERT: B   64 SER cc_start: 0.8002 (m) cc_final: 0.7773 (p)
REVERT: E   32 TYR cc_start: 0.7525 (m-80) cc_final: 0.7254 (m-80)
REVERT: C  357 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7127 (ttp80)
REVERT: C  379 CYS cc_start: 0.7421 (m) cc_final: 0.7177 (m)
REVERT: C  487 ASN cc_start: 0.6560 (t0) cc_final: 0.6274 (t0)
REVERT: C  515 PHE cc_start: 0.7971 (m-80) cc_final: 0.7605 (m-80)
REVERT: C  525 CYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3126 (p)
REVERT: D   47 TRP cc_start: 0.8452 (t60) cc_final: 0.7753 (t60)
REVERT: D   55 SER cc_start: 0.8335 (t) cc_final: 0.8063 (p)
REVERT: F   40 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6874 (m-30)
  outliers start: 26
  outliers final: 14
  residues processed: 147
  average time/residue: 0.2903
  time to fit residues: 46.8952
Evaluate side-chains
  144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   97 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0970
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0170
   chunk 8 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
C 354 ASN
C 414 GLN
C 501 ASN
F  34 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.127098 restraints weight = 9488.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.01
r_work: 0.3534 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6911  Z= 0.153
  Angle     :  0.606  12.837   9435  Z= 0.315
  Chirality :  0.044   0.194   1034
  Planarity :  0.005   0.057   1217
  Dihedral  :  5.415  27.634    978
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.49 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.28), residues: 880
  helix: -4.22 (0.38), residues: 26
  sheet: -0.21 (0.26), residues: 405
  loop : -1.30 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 100 
 TYR   0.022   0.002   TYR F  55 
 PHE   0.019   0.002   PHE F  93 
 TRP   0.014   0.002   TRP A  47 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6901)
  covalent geometry    : angle       0.60612 ( 9415)
  SS BOND              : bond        0.00494 (   10)
  SS BOND              : angle       0.68783 (   20)
  hydrogen bonds       : bond        0.03341 (  214)
  hydrogen bonds       : angle       5.67355 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLN cc_start: 0.7573 (tt0) cc_final: 0.6998 (pt0)
REVERT: B   51 ASP cc_start: 0.8031 (m-30) cc_final: 0.7723 (m-30)
REVERT: B   64 SER cc_start: 0.7987 (m) cc_final: 0.7762 (p)
REVERT: E   32 TYR cc_start: 0.7526 (m-80) cc_final: 0.7300 (m-80)
REVERT: C  357 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7095 (ttp80)
REVERT: C  379 CYS cc_start: 0.7421 (m) cc_final: 0.7178 (m)
REVERT: C  524 VAL cc_start: 0.6405 (OUTLIER) cc_final: 0.6173 (t)
REVERT: C  525 CYS cc_start: 0.4096 (OUTLIER) cc_final: 0.3152 (p)
REVERT: D   55 SER cc_start: 0.8307 (t) cc_final: 0.7983 (p)
REVERT: F    4 MET cc_start: 0.7265 (mmm) cc_final: 0.6934 (mmt)
REVERT: F   40 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6838 (m-30)
REVERT: F   79 LEU cc_start: 0.7550 (tp) cc_final: 0.7328 (tp)
  outliers start: 18
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2983
  time to fit residues: 45.4441
Evaluate side-chains
  140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0770
   chunk 45 optimal weight:    0.4980
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
F  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.142561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.128440 restraints weight = 9514.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.99
r_work: 0.3550 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6911  Z= 0.121
  Angle     :  0.577  12.556   9435  Z= 0.299
  Chirality :  0.044   0.201   1034
  Planarity :  0.004   0.055   1217
  Dihedral  :  5.077  24.367    978
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.19 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 880
  helix: -3.87 (0.55), residues: 25
  sheet:  0.06 (0.26), residues: 393
  loop : -1.14 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 100 
 TYR   0.021   0.002   TYR F  55 
 PHE   0.018   0.001   PHE F  93 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6901)
  covalent geometry    : angle       0.57645 ( 9415)
  SS BOND              : bond        0.00457 (   10)
  SS BOND              : angle       0.63593 (   20)
  hydrogen bonds       : bond        0.03116 (  214)
  hydrogen bonds       : angle       5.44133 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.6778 (OUTLIER) cc_final: 0.6478 (t)
REVERT: B   38 GLN cc_start: 0.7549 (tt0) cc_final: 0.6950 (pt0)
REVERT: B   51 ASP cc_start: 0.8050 (m-30) cc_final: 0.7667 (m-30)
REVERT: B   64 SER cc_start: 0.7958 (m) cc_final: 0.7717 (p)
REVERT: E  118 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7873 (tt)
REVERT: C  357 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7027 (ttp80)
REVERT: C  379 CYS cc_start: 0.7399 (m) cc_final: 0.7152 (m)
REVERT: C  525 CYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3170 (p)
REVERT: D   47 TRP cc_start: 0.8482 (t60) cc_final: 0.7931 (t60)
REVERT: F    4 MET cc_start: 0.7205 (mmm) cc_final: 0.7000 (mmt)
REVERT: F   40 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6831 (m-30)
REVERT: F   79 LEU cc_start: 0.7493 (tp) cc_final: 0.7287 (tp)
  outliers start: 23
  outliers final: 13
  residues processed: 138
  average time/residue: 0.2504
  time to fit residues: 38.1213
Evaluate side-chains
  137 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.126135 restraints weight = 9488.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.98
r_work: 0.3519 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   6911  Z= 0.282
  Angle     :  0.705  13.511   9435  Z= 0.370
  Chirality :  0.048   0.225   1034
  Planarity :  0.005   0.057   1217
  Dihedral  :  5.827  32.676    978
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.61 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.28), residues: 880
  helix: -4.03 (0.46), residues: 26
  sheet: -0.10 (0.26), residues: 399
  loop : -1.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 100 
 TYR   0.030   0.003   TYR F  55 
 PHE   0.024   0.002   PHE G  36 
 TRP   0.023   0.003   TRP E 113 
 HIS   0.004   0.002   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 ( 6901)
  covalent geometry    : angle       0.70421 ( 9415)
  SS BOND              : bond        0.00662 (   10)
  SS BOND              : angle       0.92410 (   20)
  hydrogen bonds       : bond        0.03911 (  214)
  hydrogen bonds       : angle       5.98210 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLN cc_start: 0.7604 (tt0) cc_final: 0.7055 (pt0)
REVERT: B   51 ASP cc_start: 0.8068 (m-30) cc_final: 0.7596 (m-30)
REVERT: B   64 SER cc_start: 0.8031 (m) cc_final: 0.7783 (p)
REVERT: C  357 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7020 (ttp80)
REVERT: C  379 CYS cc_start: 0.7441 (m) cc_final: 0.7208 (m)
REVERT: D   47 TRP cc_start: 0.8519 (t60) cc_final: 0.8284 (t60)
REVERT: F   40 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6881 (m-30)
REVERT: F   79 LEU cc_start: 0.7650 (tp) cc_final: 0.7448 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 143
  average time/residue: 0.2271
  time to fit residues: 35.8051
Evaluate side-chains
  145 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0010
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
F  34 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128584 restraints weight = 9318.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.95
r_work: 0.3555 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6911  Z= 0.143
  Angle     :  0.618  13.009   9435  Z= 0.319
  Chirality :  0.044   0.196   1034
  Planarity :  0.005   0.054   1217
  Dihedral  :  5.331  30.120    978
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.16 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.28), residues: 880
  helix: -3.84 (0.54), residues: 26
  sheet:  0.04 (0.26), residues: 397
  loop : -1.21 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 100 
 TYR   0.023   0.002   TYR F  55 
 PHE   0.019   0.002   PHE F  93 
 TRP   0.013   0.002   TRP E 113 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6901)
  covalent geometry    : angle       0.61108 ( 9415)
  SS BOND              : bond        0.00565 (   10)
  SS BOND              : angle       2.05692 (   20)
  hydrogen bonds       : bond        0.03321 (  214)
  hydrogen bonds       : angle       5.57958 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.6651 (OUTLIER) cc_final: 0.6383 (t)
REVERT: B   38 GLN cc_start: 0.7551 (tt0) cc_final: 0.6955 (pt0)
REVERT: B   51 ASP cc_start: 0.8016 (m-30) cc_final: 0.7581 (m-30)
REVERT: B   64 SER cc_start: 0.8019 (m) cc_final: 0.7794 (p)
REVERT: G   94 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5507 (t80)
REVERT: C  357 ARG cc_start: 0.7655 (ttp80) cc_final: 0.6995 (ttp80)
REVERT: C  379 CYS cc_start: 0.7402 (m) cc_final: 0.7166 (m)
REVERT: C  525 CYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3210 (p)
REVERT: F   40 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6870 (m-30)
REVERT: F   79 LEU cc_start: 0.7480 (tp) cc_final: 0.7280 (tp)
  outliers start: 20
  outliers final: 14
  residues processed: 137
  average time/residue: 0.2822
  time to fit residues: 42.2733
Evaluate side-chains
  139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   94 TYR
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
F  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.142522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.128272 restraints weight = 9404.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.99
r_work: 0.3550 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6911  Z= 0.162
  Angle     :  0.621  12.885   9435  Z= 0.321
  Chirality :  0.044   0.188   1034
  Planarity :  0.005   0.060   1217
  Dihedral  :  5.347  29.680    978
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.16 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.28), residues: 880
  helix: -3.75 (0.56), residues: 26
  sheet:  0.14 (0.27), residues: 392
  loop : -1.25 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 100 
 TYR   0.024   0.002   TYR F  55 
 PHE   0.016   0.002   PHE D  37 
 TRP   0.014   0.002   TRP E 113 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6901)
  covalent geometry    : angle       0.61624 ( 9415)
  SS BOND              : bond        0.00499 (   10)
  SS BOND              : angle       1.76599 (   20)
  hydrogen bonds       : bond        0.03360 (  214)
  hydrogen bonds       : angle       5.59377 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.6670 (OUTLIER) cc_final: 0.6410 (t)
REVERT: B   38 GLN cc_start: 0.7556 (tt0) cc_final: 0.6966 (pt0)
REVERT: B   51 ASP cc_start: 0.8049 (m-30) cc_final: 0.7613 (m-30)
REVERT: B   64 SER cc_start: 0.8054 (m) cc_final: 0.7806 (p)
REVERT: G   94 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.5482 (t80)
REVERT: C  357 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7019 (ttp80)
REVERT: C  379 CYS cc_start: 0.7392 (m) cc_final: 0.7157 (m)
REVERT: F   40 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6824 (m-30)
REVERT: F   79 LEU cc_start: 0.7505 (tp) cc_final: 0.7302 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 135
  average time/residue: 0.2568
  time to fit residues: 38.1640
Evaluate side-chains
  141 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   94 TYR
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 79 optimal weight:    0.4980
   chunk 39 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
F  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.142596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128600 restraints weight = 9410.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.97
r_work: 0.3553 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6911  Z= 0.165
  Angle     :  0.621  12.941   9435  Z= 0.321
  Chirality :  0.044   0.187   1034
  Planarity :  0.005   0.058   1217
  Dihedral  :  5.337  29.338    978
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.88 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 880
  helix: -3.28 (0.69), residues: 19
  sheet:  0.12 (0.26), residues: 397
  loop : -1.24 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 100 
 TYR   0.024   0.002   TYR F  55 
 PHE   0.016   0.002   PHE D  37 
 TRP   0.015   0.002   TRP E 113 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6901)
  covalent geometry    : angle       0.61717 ( 9415)
  SS BOND              : bond        0.00476 (   10)
  SS BOND              : angle       1.55088 (   20)
  hydrogen bonds       : bond        0.03363 (  214)
  hydrogen bonds       : angle       5.59366 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.6631 (OUTLIER) cc_final: 0.6384 (t)
REVERT: B   38 GLN cc_start: 0.7552 (tt0) cc_final: 0.6958 (pt0)
REVERT: B   51 ASP cc_start: 0.8032 (m-30) cc_final: 0.7677 (m-30)
REVERT: B   64 SER cc_start: 0.8048 (m) cc_final: 0.7802 (p)
REVERT: G   94 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.5469 (t80)
REVERT: C  379 CYS cc_start: 0.7385 (m) cc_final: 0.7152 (m)
REVERT: C  403 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6567 (ptp-110)
REVERT: F   40 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6847 (m-30)
REVERT: F   79 LEU cc_start: 0.7532 (tp) cc_final: 0.7325 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 135
  average time/residue: 0.2620
  time to fit residues: 38.9079
Evaluate side-chains
  140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   94 TYR
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  403 ARG
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0020
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    0.3980
   chunk 16 optimal weight:    0.2980
   chunk 85 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 69 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.2988

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

Flipped N/Q/H residues before XYZ refinement:
F  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.143965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.129738 restraints weight = 9407.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.99
r_work: 0.3565 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6911  Z= 0.113
  Angle     :  0.586  12.720   9435  Z= 0.298
  Chirality :  0.043   0.159   1034
  Planarity :  0.005   0.059   1217
  Dihedral  :  5.009  26.375    978
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.30 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.28), residues: 880
  helix: -3.12 (0.72), residues: 19
  sheet:  0.36 (0.27), residues: 387
  loop : -1.15 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 100 
 TYR   0.020   0.001   TYR F  55 
 PHE   0.016   0.001   PHE F  93 
 TRP   0.012   0.001   TRP E 113 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6901)
  covalent geometry    : angle       0.58311 ( 9415)
  SS BOND              : bond        0.00394 (   10)
  SS BOND              : angle       1.32242 (   20)
  hydrogen bonds       : bond        0.03035 (  214)
  hydrogen bonds       : angle       5.34250 (  537)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.6558 (OUTLIER) cc_final: 0.6314 (t)
REVERT: B   38 GLN cc_start: 0.7522 (tt0) cc_final: 0.6913 (pt0)
REVERT: B   51 ASP cc_start: 0.8024 (m-30) cc_final: 0.7707 (m-30)
REVERT: B   64 SER cc_start: 0.8008 (m) cc_final: 0.7757 (p)
REVERT: E   60 TYR cc_start: 0.7915 (m-80) cc_final: 0.7021 (m-80)
REVERT: G   94 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.5366 (t80)
REVERT: C  379 CYS cc_start: 0.7397 (m) cc_final: 0.7164 (m)
REVERT: F   40 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6858 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 130
  average time/residue: 0.2440
  time to fit residues: 35.1563
Evaluate side-chains
  134 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain E residue  107 MET
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   94 TYR
Chi-restraints excluded: chain C residue  343 ASN
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  438 SER
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   40 ASP
Chi-restraints excluded: chain F residue   71 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.142096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128088 restraints weight = 9276.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.95
r_work: 0.3539 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6911  Z= 0.211
  Angle     :  0.667  12.844   9435  Z= 0.342
  Chirality :  0.045   0.191   1034
  Planarity :  0.005   0.058   1217
  Dihedral  :  5.477  30.083    978
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.16 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.28), residues: 880
  helix: -3.19 (0.67), residues: 19
  sheet:  0.20 (0.26), residues: 396
  loop : -1.31 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 100 
 TYR   0.028   0.002   TYR F  55 
 PHE   0.019   0.002   PHE G  36 
 TRP   0.018   0.002   TRP E 113 
 HIS   0.004   0.002   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 6901)
  covalent geometry    : angle       0.66359 ( 9415)
  SS BOND              : bond        0.00550 (   10)
  SS BOND              : angle       1.53689 (   20)
  hydrogen bonds       : bond        0.03536 (  214)
  hydrogen bonds       : angle       5.68410 (  537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2267.04 seconds
wall clock time: 39 minutes 25.23 seconds (2365.23 seconds total)