Starting phenix.real_space_refine
on Sun Aug 24 05:50:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ban_44407/08_2025/9ban_44407.map"
  }
  resolution = 3.39
  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=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    5545      2.51       5
     N    1516      2.21       5
     O    1715      1.98       5
     H    8684      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17505
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1405
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 6, 'TRANS': 84}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1546
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
      Conformer: "B"
        Number of residues, atoms: 102, 1527
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
          bond proxies already assigned to first conformer: 1521
    Chain: "C"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 340
          Classifications: {'peptide': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 19}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 1458
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 97, 1439
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 88}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 97, 1439
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 88}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1431
    Chain: "E"
      Number of atoms: 3141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3141
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3242
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202}
    Chain: "G"
      Number of atoms: 3131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3131
          Classifications: {'peptide': 212}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU%NH1NOTPRO:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "H"
      Number of atoms: 3242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3242
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202}
  Time building chain proxies: 3.45, per 1000 atoms: 0.20
  Number of scatterers: 17505
  At special positions: 0
  Unit cell: (88.102, 100.688, 132.602, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      45     16.00
     O    1715      8.00
     N    1516      7.00
     C    5545      6.00
     H    8684      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 462 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 557 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 492 " - pdb=" SG  CYS B 559 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 462 " - pdb=" SG  CYS D 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 488 " - pdb=" SG  CYS D 557 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 492 " - pdb=" SG  CYS D 559 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 166 " - pdb=" SG  CYS E 221 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  43 " - pdb=" SG  CYS F 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 153 " - pdb=" SG  CYS F 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  41 " - pdb=" SG  CYS G 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 166 " - pdb=" SG  CYS G 221 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  43 " - pdb=" SG  CYS H 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 153 " - pdb=" SG  CYS H 213 " 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: 1.44
  Conformation dependent library (CDL) restraints added in 512.0 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2186

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 26 sheets defined
      12.4% alpha, 35.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 290 through 302
    Processing helix  chain 'A' and resid 376 through 393
      removed outlier: 3.692A  pdb=" N   ALA A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 393 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 420 through 439
      removed outlier: 3.904A  pdb=" N   ALA A 424 " --> pdb=" O   ASP A 420 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 425 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 439 " --> pdb=" O   ARG A 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 517
      removed outlier: 3.826A  pdb=" N   GLY B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 302
    Processing helix  chain 'D' and resid 504 through 517
      removed outlier: 3.699A  pdb=" N   GLY D 517 " --> pdb=" O   MET D 513 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 47 through 51
    Processing helix  chain 'E' and resid 182 through 184
      No H-bonds generated for 'chain 'E' and resid 182 through 184'
    Processing helix  chain 'F' and resid 140 through 147
    Processing helix  chain 'F' and resid 202 through 208
      removed outlier: 3.793A  pdb=" N   HIS F 208 " --> pdb=" O   GLU F 204 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 51
    Processing helix  chain 'G' and resid 182 through 184
      No H-bonds generated for 'chain 'G' and resid 182 through 184'
    Processing helix  chain 'H' and resid 140 through 147
    Processing helix  chain 'H' and resid 202 through 208
      removed outlier: 3.553A  pdb=" N   ARG H 207 " --> pdb=" O   ASP H 203 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   HIS H 208 " --> pdb=" O   GLU H 204 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 463 through 465
    Processing sheet with id=AA2, first strand: chain 'B' and resid 468 through 470
    Processing sheet with id=AA3, first strand: chain 'B' and resid 477 through 479
      removed outlier: 6.162A  pdb=" N   ALA B 532 " --> pdb=" O   ASN B 551 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN B 551 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 519 through 520
      removed outlier: 3.580A  pdb=" N   ALA B 519 " --> pdb=" O   ALA G 125 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA G 125 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 520
      removed outlier: 3.580A  pdb=" N   ALA B 519 " --> pdb=" O   ALA G 125 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA G 125 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY G  68 " --> pdb=" O   TRP G  55 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LYS G  57 " --> pdb=" O   TRP G  66 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   TRP G  66 " --> pdb=" O   LYS G  57 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   LEU G  64 " --> pdb=" O   ARG G  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 525 through 528
      removed outlier: 3.649A  pdb=" N   VAL B 527 " --> pdb=" O   GLY B 558 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 463 through 465
    Processing sheet with id=AA8, first strand: chain 'D' and resid 468 through 470
    Processing sheet with id=AA9, first strand: chain 'D' and resid 477 through 479
      removed outlier: 6.113A  pdb=" N   ALA D 532 " --> pdb=" O   ASN D 551 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN D 551 " --> pdb=" O   ALA D 532 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 519 through 520
      removed outlier: 3.563A  pdb=" N   ALA D 519 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA E 125 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 519 through 520
      removed outlier: 3.563A  pdb=" N   ALA D 519 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA E 125 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY E  68 " --> pdb=" O   TRP E  55 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LYS E  57 " --> pdb=" O   TRP E  66 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   TRP E  66 " --> pdb=" O   LYS E  57 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG E  59 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   LEU E  64 " --> pdb=" O   ARG E  59 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 525 through 528
      removed outlier: 3.657A  pdb=" N   VAL D 527 " --> pdb=" O   GLY D 558 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 150
      removed outlier: 3.593A  pdb=" N   GLY E 165 " --> pdb=" O   LEU E 150 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 177 through 180
    Processing sheet with id=AB7, first strand: chain 'F' and resid 24 through 27
      removed outlier: 3.642A  pdb=" N   PHE F  91 " --> pdb=" O   CYS F  43 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASP F  90 " --> pdb=" O   TYR F  87 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 68
      removed outlier: 5.585A  pdb=" N   LEU F  66 " --> pdb=" O   GLN F  57 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   GLN F  57 " --> pdb=" O   LEU F  66 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 133 through 137
    Processing sheet with id=AC1, first strand: chain 'F' and resid 173 through 174
      removed outlier: 3.713A  pdb=" N   ARG F 174 " --> pdb=" O   TRP F 167 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TRP F 167 " --> pdb=" O   ARG F 174 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 24 through 25
    Processing sheet with id=AC3, first strand: chain 'G' and resid 146 through 150
      removed outlier: 3.583A  pdb=" N   GLY G 165 " --> pdb=" O   LEU G 150 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 177 through 180
    Processing sheet with id=AC5, first strand: chain 'H' and resid 24 through 27
      removed outlier: 3.632A  pdb=" N   PHE H  91 " --> pdb=" O   CYS H  43 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP H  90 " --> pdb=" O   TYR H  87 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 65 through 68
      removed outlier: 5.630A  pdb=" N   LEU H  66 " --> pdb=" O   GLN H  57 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLN H  57 " --> pdb=" O   LEU H  66 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 133 through 137
    Processing sheet with id=AC8, first strand: chain 'H' and resid 164 through 169

    343 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.53

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8685
        1.03 -     1.23: 354
        1.23 -     1.43: 3390
        1.43 -     1.63: 5208
        1.63 -     1.83: 59
  Bond restraints: 17696
  Sorted by residual:
  bond pdb=" C   ASN F  73 "
       pdb=" O   ASN F  73 "
    ideal  model  delta    sigma   weight residual
    1.235  1.162  0.073 1.14e-02 7.69e+03 4.07e+01
  bond pdb=" CA  TYR F  75 "
       pdb=" C   TYR F  75 "
    ideal  model  delta    sigma   weight residual
    1.523  1.455  0.069 1.34e-02 5.57e+03 2.62e+01
  bond pdb=" N   GLU G  20 "
       pdb=" H1  GLU G  20 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C   TYR F  75 "
       pdb=" O   TYR F  75 "
    ideal  model  delta    sigma   weight residual
    1.235  1.178  0.057 1.26e-02 6.30e+03 2.06e+01
  bond pdb=" N   SER F  21 "
       pdb=" H3  SER F  21 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 17691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.11: 31930
        5.11 -    10.21: 7
       10.21 -    15.32: 2
       15.32 -    20.42: 2
       20.42 -    25.53: 1
  Bond angle restraints: 31942
  Sorted by residual:
  angle pdb=" H1  SER F  21 "
        pdb=" N   SER F  21 "
        pdb=" H3  SER F  21 "
      ideal   model   delta    sigma   weight residual
     109.47   83.94   25.53 3.00e+00 1.11e-01 7.24e+01
  angle pdb=" CA  SER F  72 "
        pdb=" C   SER F  72 "
        pdb=" N   ASN F  73 "
      ideal   model   delta    sigma   weight residual
     115.92  124.16   -8.24 1.28e+00 6.10e-01 4.14e+01
  angle pdb=" N   ASN F  73 "
        pdb=" CA  ASN F  73 "
        pdb=" C   ASN F  73 "
      ideal   model   delta    sigma   weight residual
     108.34  100.44    7.90 1.31e+00 5.83e-01 3.64e+01
  angle pdb=" H1  SER F  21 "
        pdb=" N   SER F  21 "
        pdb=" H2  SER F  21 "
      ideal   model   delta    sigma   weight residual
     109.47  126.43  -16.96 3.00e+00 1.11e-01 3.20e+01
  angle pdb=" H1  SER H  21 "
        pdb=" N   SER H  21 "
        pdb=" H3  SER H  21 "
      ideal   model   delta    sigma   weight residual
     109.47   92.71   16.76 3.00e+00 1.11e-01 3.12e+01
  ... (remaining 31937 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 7538
       16.84 -    33.68: 679
       33.68 -    50.52: 225
       50.52 -    67.35: 49
       67.35 -    84.19: 14
  Dihedral angle restraints: 8505
    sinusoidal: 4611
      harmonic: 3894
  Sorted by residual:
  dihedral pdb=" CB  CYS G 166 "
           pdb=" SG  CYS G 166 "
           pdb=" SG  CYS G 221 "
           pdb=" CB  CYS G 221 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.45   36.55     1      1.00e+01 1.00e-02 1.89e+01
  dihedral pdb=" CB  CYS E 166 "
           pdb=" SG  CYS E 166 "
           pdb=" SG  CYS E 221 "
           pdb=" CB  CYS E 221 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.52   34.48     1      1.00e+01 1.00e-02 1.69e+01
  dihedral pdb=" NE  ARG F  74 "
           pdb=" CZ  ARG F  74 "
           pdb=" NH1 ARG F  74 "
           pdb="HH12 ARG F  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.47  -76.47     2      2.00e+01 2.50e-03 1.13e+01
  ... (remaining 8502 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 821
       0.030 -    0.060: 414
       0.060 -    0.090: 80
       0.090 -    0.120: 79
       0.120 -    0.150: 32
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CA  ILE F  41 "
            pdb=" N   ILE F  41 "
            pdb=" C   ILE F  41 "
            pdb=" CB  ILE F  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.59e-01
  chirality pdb=" CA  ILE E 119 "
            pdb=" N   ILE E 119 "
            pdb=" C   ILE E 119 "
            pdb=" CB  ILE E 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  ILE F 163 "
            pdb=" N   ILE F 163 "
            pdb=" C   ILE F 163 "
            pdb=" CB  ILE F 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1423 not shown)

  Planarity restraints: 2646
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  74 "   -0.412 9.50e-02 1.11e+02   3.73e-01 2.73e+03
        pdb=" NE  ARG F  74 "   -0.124 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  74 "   -0.029 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  74 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  74 "    0.027 2.00e-02 2.50e+03
        pdb="HH11 ARG F  74 "   -0.706 2.00e-02 2.50e+03
        pdb="HH12 ARG F  74 "    0.750 2.00e-02 2.50e+03
        pdb="HH21 ARG F  74 "    0.009 2.00e-02 2.50e+03
        pdb="HH22 ARG F  74 "    0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN F  73 "   -0.244 2.00e-02 2.50e+03   3.21e-01 1.55e+03
        pdb=" CG  ASN F  73 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD1 ASN F  73 "    0.257 2.00e-02 2.50e+03
        pdb=" ND2 ASN F  73 "   -0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN F  73 "    0.499 2.00e-02 2.50e+03
        pdb="HD22 ASN F  73 "   -0.494 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG G  59 "    0.035 5.00e-02 4.00e+02   5.28e-02 4.45e+00
        pdb=" N   PRO G  60 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2643 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 3010
        2.28 -     2.86: 37270
        2.86 -     3.44: 37530
        3.44 -     4.02: 54528
        4.02 -     4.60: 81576
  Nonbonded interactions: 213914
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 541 "
            pdb=" H   GLU B 541 "
     model   vdw
     1.697 2.450
  nonbonded pdb=" HE  ARG A 312 "
            pdb=" OD1 ASP B 470 "
     model   vdw
     1.713 2.450
  nonbonded pdb="HD22 ASN H 209 "
            pdb=" OD1 ASN H 231 "
     model   vdw
     1.715 2.450
  nonbonded pdb=" OD1 ASP F 203 "
            pdb=" H   GLU F 204 "
     model   vdw
     1.729 2.450
  nonbonded pdb=" OD1 ASP H 203 "
            pdb=" H   GLU H 204 "
     model   vdw
     1.757 2.450
  ... (remaining 213909 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 459 through 472 or (resid 473 and (name N or name CA or na \ 
me C or name O or name CB or name H or name HA )) or resid 476 through 501 or re \ 
sid 503 through 540 or resid 544 through 560))
  selection = (chain 'D' and (resid 459 through 501 or resid 503 through 560))
}
ncs_group {
  reference = (chain 'E' and ((resid 20 and (name N or name CA or name C or name O or name CB  \ 
or name H1 or name HA )) or resid 21 through 238))
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

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=0.35 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:             18.850
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     16.560
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
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   0.073   9024  Z= 0.195
  Angle     :  0.614   8.239  12304  Z= 0.340
  Chirality :  0.044   0.150   1426
  Planarity :  0.004   0.089   1565
  Dihedral  : 14.568  84.192   3236
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.31 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.51 (0.26), residues: 1134
  helix:  2.54 (0.48), residues: 117
  sheet:  0.50 (0.24), residues: 513
  loop : -2.03 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 391 
 TYR   0.019   0.001   TYR F  69 
 PHE   0.013   0.002   PHE F 228 
 TRP   0.007   0.001   TRP H 182 
 HIS   0.003   0.001   HIS B 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9010)
  covalent geometry    : angle       0.60961 (12276)
  SS BOND              : bond        0.00650 (   14)
  SS BOND              : angle       1.69801 (   28)
  hydrogen bonds       : bond        0.09204 (  335)
  hydrogen bonds       : angle       4.50295 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  88 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.2482
  time to fit residues: 28.5327
Evaluate side-chains
  77 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
D 514 GLN
F 209 ASN
H 209 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126020 restraints weight = 38502.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.23
r_work: 0.3389 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.0675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9024  Z= 0.123
  Angle     :  0.537   4.550  12304  Z= 0.284
  Chirality :  0.043   0.161   1426
  Planarity :  0.004   0.052   1565
  Dihedral  :  4.166  23.735   1253
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.56 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.50 (0.26), residues: 1134
  helix:  2.60 (0.46), residues: 117
  sheet:  0.55 (0.24), residues: 515
  loop : -2.11 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 465 
 TYR   0.011   0.001   TYR G 114 
 PHE   0.010   0.001   PHE F  93 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.002   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9010)
  covalent geometry    : angle       0.53406 (12276)
  SS BOND              : bond        0.00639 (   14)
  SS BOND              : angle       1.37758 (   28)
  hydrogen bonds       : bond        0.03597 (  335)
  hydrogen bonds       : angle       4.27990 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  203 ASP cc_start: 0.8060 (p0) cc_final: 0.7847 (p0)
REVERT: F  209 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7813 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2244
  time to fit residues: 28.1194
Evaluate side-chains
  87 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  209 ASN
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
F 209 ASN
H 209 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.145102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120548 restraints weight = 42628.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.64
r_work: 0.3306 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9024  Z= 0.155
  Angle     :  0.558   4.391  12304  Z= 0.298
  Chirality :  0.044   0.155   1426
  Planarity :  0.004   0.053   1565
  Dihedral  :  4.306  20.025   1253
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.74 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.54 (0.26), residues: 1134
  helix:  2.65 (0.45), residues: 120
  sheet:  0.53 (0.24), residues: 515
  loop : -2.19 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  74 
 TYR   0.012   0.001   TYR G 114 
 PHE   0.013   0.002   PHE F  93 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.003   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9010)
  covalent geometry    : angle       0.55342 (12276)
  SS BOND              : bond        0.00809 (   14)
  SS BOND              : angle       1.56168 (   28)
  hydrogen bonds       : bond        0.04085 (  335)
  hydrogen bonds       : angle       4.38122 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  203 ASP cc_start: 0.8162 (p0) cc_final: 0.7929 (p0)
  outliers start: 22
  outliers final: 18
  residues processed: 99
  average time/residue: 0.2259
  time to fit residues: 30.2880
Evaluate side-chains
  94 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  109 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue   94 SER
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  199 ASP
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  209 ASN
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
F 209 ASN
H 209 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.147134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124910 restraints weight = 35441.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.15
r_work: 0.3383 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9024  Z= 0.107
  Angle     :  0.510   3.854  12304  Z= 0.270
  Chirality :  0.043   0.152   1426
  Planarity :  0.004   0.054   1565
  Dihedral  :  4.195  20.484   1253
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.05 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.43 (0.26), residues: 1134
  helix:  2.94 (0.46), residues: 117
  sheet:  0.55 (0.25), residues: 515
  loop : -2.08 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.008   0.001   TYR G 114 
 PHE   0.010   0.001   PHE F 228 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.004   0.001   HIS H 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9010)
  covalent geometry    : angle       0.50719 (12276)
  SS BOND              : bond        0.00634 (   14)
  SS BOND              : angle       1.19357 (   28)
  hydrogen bonds       : bond        0.03366 (  335)
  hydrogen bonds       : angle       4.30101 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  203 ASP cc_start: 0.8095 (p0) cc_final: 0.7828 (p0)
  outliers start: 19
  outliers final: 18
  residues processed: 94
  average time/residue: 0.2032
  time to fit residues: 26.1251
Evaluate side-chains
  96 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  190 SER
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  199 ASP
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  123 LEU
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 107 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
F  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.144877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.122282 restraints weight = 37105.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.22
r_work: 0.3343 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9024  Z= 0.142
  Angle     :  0.541   4.202  12304  Z= 0.289
  Chirality :  0.043   0.150   1426
  Planarity :  0.004   0.055   1565
  Dihedral  :  4.276  19.857   1253
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.95 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.50 (0.26), residues: 1134
  helix:  2.77 (0.46), residues: 120
  sheet:  0.51 (0.24), residues: 515
  loop : -2.13 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.011   0.001   TYR G 114 
 PHE   0.012   0.001   PHE F  93 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.004   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9010)
  covalent geometry    : angle       0.53749 (12276)
  SS BOND              : bond        0.00737 (   14)
  SS BOND              : angle       1.41975 (   28)
  hydrogen bonds       : bond        0.03817 (  335)
  hydrogen bonds       : angle       4.35393 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  203 ASP cc_start: 0.8134 (p0) cc_final: 0.7878 (p0)
  outliers start: 29
  outliers final: 26
  residues processed: 106
  average time/residue: 0.1778
  time to fit residues: 25.9053
Evaluate side-chains
  104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  127 ASP
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue  109 GLN
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  190 SER
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  199 ASP
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain G residue  232 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  123 LEU
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124312 restraints weight = 39875.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.30
r_work: 0.3372 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9024  Z= 0.098
  Angle     :  0.496   3.944  12304  Z= 0.261
  Chirality :  0.042   0.147   1426
  Planarity :  0.004   0.053   1565
  Dihedral  :  4.117  18.090   1253
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.26 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.42 (0.26), residues: 1134
  helix:  2.85 (0.46), residues: 120
  sheet:  0.52 (0.24), residues: 505
  loop : -1.98 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.007   0.001   TYR H  69 
 PHE   0.009   0.001   PHE F 228 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.002   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9010)
  covalent geometry    : angle       0.49384 (12276)
  SS BOND              : bond        0.00562 (   14)
  SS BOND              : angle       1.15295 (   28)
  hydrogen bonds       : bond        0.03099 (  335)
  hydrogen bonds       : angle       4.25150 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  488 CYS cc_start: 0.7858 (m) cc_final: 0.7640 (m)
REVERT: F  203 ASP cc_start: 0.8105 (p0) cc_final: 0.7852 (p0)
REVERT: F  225 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8291 (p)
  outliers start: 24
  outliers final: 17
  residues processed: 103
  average time/residue: 0.1964
  time to fit residues: 27.9193
Evaluate side-chains
  102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  127 ASP
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.145890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.122858 restraints weight = 40461.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.34
r_work: 0.3344 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9024  Z= 0.122
  Angle     :  0.518   4.708  12304  Z= 0.275
  Chirality :  0.043   0.149   1426
  Planarity :  0.004   0.053   1565
  Dihedral  :  4.160  19.089   1253
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.36 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.44 (0.26), residues: 1134
  helix:  2.87 (0.46), residues: 120
  sheet:  0.51 (0.24), residues: 515
  loop : -2.06 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.009   0.001   TYR H  69 
 PHE   0.011   0.001   PHE H  93 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.003   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9010)
  covalent geometry    : angle       0.51404 (12276)
  SS BOND              : bond        0.00672 (   14)
  SS BOND              : angle       1.36491 (   28)
  hydrogen bonds       : bond        0.03500 (  335)
  hydrogen bonds       : angle       4.27690 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  513 MET cc_start: 0.8596 (tpp) cc_final: 0.8360 (ttm)
REVERT: D  488 CYS cc_start: 0.7833 (m) cc_final: 0.7610 (m)
REVERT: F  203 ASP cc_start: 0.8113 (p0) cc_final: 0.7907 (p0)
REVERT: F  225 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8329 (p)
  outliers start: 27
  outliers final: 25
  residues processed: 103
  average time/residue: 0.2065
  time to fit residues: 28.9653
Evaluate side-chains
  107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain D residue  526 CYS
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  127 ASP
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  190 SER
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue   74 ASN
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  199 ASP
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.0980
   chunk 102 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0870
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
F 209 ASN
G 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.149000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.125838 restraints weight = 37304.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.34
r_work: 0.3419 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9024  Z= 0.081
  Angle     :  0.467   3.980  12304  Z= 0.244
  Chirality :  0.042   0.151   1426
  Planarity :  0.004   0.052   1565
  Dihedral  :  3.899  15.236   1253
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.18 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.29 (0.26), residues: 1134
  helix:  3.22 (0.47), residues: 117
  sheet:  0.66 (0.25), residues: 469
  loop : -1.84 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.006   0.001   TYR H  69 
 PHE   0.008   0.001   PHE F 228 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.002   0.000   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 9010)
  covalent geometry    : angle       0.46583 (12276)
  SS BOND              : bond        0.00407 (   14)
  SS BOND              : angle       0.82315 (   28)
  hydrogen bonds       : bond        0.02528 (  335)
  hydrogen bonds       : angle       4.06887 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  488 CYS cc_start: 0.7802 (m) cc_final: 0.7563 (m)
REVERT: F  203 ASP cc_start: 0.8063 (p0) cc_final: 0.7839 (p0)
REVERT: F  225 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8284 (p)
REVERT: H  143 GLN cc_start: 0.8267 (tp40) cc_final: 0.7516 (tt0)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1991
  time to fit residues: 25.9972
Evaluate side-chains
  95 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.145372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122911 restraints weight = 37379.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.21
r_work: 0.3364 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9024  Z= 0.134
  Angle     :  0.522   4.983  12304  Z= 0.278
  Chirality :  0.043   0.149   1426
  Planarity :  0.004   0.053   1565
  Dihedral  :  4.096  19.877   1253
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.67 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1134
  helix:  2.93 (0.47), residues: 120
  sheet:  0.54 (0.25), residues: 505
  loop : -1.89 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 475 
 TYR   0.010   0.001   TYR E 114 
 PHE   0.013   0.001   PHE F 158 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9010)
  covalent geometry    : angle       0.51859 (12276)
  SS BOND              : bond        0.00694 (   14)
  SS BOND              : angle       1.40818 (   28)
  hydrogen bonds       : bond        0.03618 (  335)
  hydrogen bonds       : angle       4.20813 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  488 CYS cc_start: 0.7775 (m) cc_final: 0.7571 (m)
REVERT: F  225 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8350 (p)
REVERT: H  143 GLN cc_start: 0.8386 (tp40) cc_final: 0.7630 (tt0)
  outliers start: 21
  outliers final: 19
  residues processed: 100
  average time/residue: 0.1940
  time to fit residues: 26.1827
Evaluate side-chains
  100 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  526 CYS
Chi-restraints excluded: chain D residue  526 CYS
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain G residue  232 VAL
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.145663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122804 restraints weight = 38212.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.27
r_work: 0.3357 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9024  Z= 0.127
  Angle     :  0.517   3.852  12304  Z= 0.275
  Chirality :  0.043   0.147   1426
  Planarity :  0.004   0.052   1565
  Dihedral  :  4.163  19.796   1253
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.46 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.39 (0.26), residues: 1134
  helix:  2.80 (0.46), residues: 120
  sheet:  0.52 (0.24), residues: 505
  loop : -1.93 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 207 
 TYR   0.009   0.001   TYR H  69 
 PHE   0.012   0.001   PHE H  93 
 TRP   0.005   0.001   TRP D 494 
 HIS   0.003   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9010)
  covalent geometry    : angle       0.51327 (12276)
  SS BOND              : bond        0.00671 (   14)
  SS BOND              : angle       1.33937 (   28)
  hydrogen bonds       : bond        0.03508 (  335)
  hydrogen bonds       : angle       4.22471 (  903)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  422 is missing expected H atoms. Skipping.
Residue VAL  298 is missing expected H atoms. Skipping.
Residue LEU  301 is missing expected H atoms. Skipping.
Residue ALA  473 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  488 CYS cc_start: 0.7783 (m) cc_final: 0.7563 (m)
REVERT: F  225 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8347 (p)
REVERT: H  143 GLN cc_start: 0.8398 (tp40) cc_final: 0.7649 (tt0)
  outliers start: 24
  outliers final: 21
  residues processed: 100
  average time/residue: 0.2094
  time to fit residues: 28.6389
Evaluate side-chains
  100 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  526 CYS
Chi-restraints excluded: chain D residue  526 CYS
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  190 SER
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue  127 ASP
Chi-restraints excluded: chain G residue  179 THR
Chi-restraints excluded: chain G residue  182 SER
Chi-restraints excluded: chain G residue  204 SER
Chi-restraints excluded: chain G residue  232 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  195 SER
Chi-restraints excluded: chain H residue  212 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 104 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
F 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.147246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123910 restraints weight = 40505.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.41
r_work: 0.3378 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9024  Z= 0.095
  Angle     :  0.494   5.281  12304  Z= 0.260
  Chirality :  0.042   0.147   1426
  Planarity :  0.004   0.053   1565
  Dihedral  :  4.045  18.101   1253
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.77 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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 aren not related in a simple way.
  whole: -0.37 (0.26), residues: 1134
  helix:  2.92 (0.47), residues: 120
  sheet:  0.62 (0.25), residues: 469
  loop : -1.87 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.008   0.001   TYR H  69 
 PHE   0.009   0.001   PHE H  93 
 TRP   0.006   0.001   TRP D 494 
 HIS   0.002   0.001   HIS G  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9010)
  covalent geometry    : angle       0.49153 (12276)
  SS BOND              : bond        0.00537 (   14)
  SS BOND              : angle       1.06128 (   28)
  hydrogen bonds       : bond        0.02989 (  335)
  hydrogen bonds       : angle       4.11810 (  903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4408.22 seconds
wall clock time: 75 minutes 27.87 seconds (4527.87 seconds total)