Starting phenix.real_space_refine
on Wed Apr 30 12:06:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8v_36081/04_2025/8j8v_36081.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      20      5.16       5
     C    5963      2.51       5
     N    1616      2.21       5
     O    1824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9437
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2890
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
    Chain: "C"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 800
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 914
          Classifications: {'peptide': 118}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114}
    Chain: "E"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 805
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2890
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "G"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 115
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 115
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 6.33, per 1000 atoms: 0.67
  Number of scatterers: 9437
  At special positions: 0
  Unit cell: (135.569, 86.3707, 104.957, 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      20     16.00
     P      14     15.00
     O    1824      8.00
     N    1616      7.00
     C    5963      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2258

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 22 sheets defined
      5.5% alpha, 46.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 110
    Processing helix  chain 'A' and resid 393 through 408
      removed outlier: 3.514A  pdb=" N   LYS A 408 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 4.056A  pdb=" N   THR B  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 4.042A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 110
    Processing helix  chain 'F' and resid 393 through 408
    Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118
    Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29
      removed outlier: 4.003A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 10.298A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP A 144 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A  88 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL A  56 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   GLN A  86 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU A  58 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   ASN A  84 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL A  60 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ILE A  82 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   PHE A  62 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   LEU A  80 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29
      removed outlier: 4.003A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 10.298A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190
      removed outlier: 3.655A  pdb=" N   SER A 203 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN A 223 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209
      removed outlier: 3.600A  pdb=" N   VAL A 336 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 342 " --> pdb=" O   TYR A 322 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   TYR A 322 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.411A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   GLU A 258 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   VAL A 234 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLN A 256 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 236 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.504A  pdb=" N   GLY B  13 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   SER B  35 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   SER B  55 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ILE B  37 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   SER B  53 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.504A  pdb=" N   GLY B  13 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR B 112 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.611A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 13
      removed outlier: 3.531A  pdb=" N   LEU C  12 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13
      removed outlier: 3.531A  pdb=" N   LEU C  12 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR C  98 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 10
      removed outlier: 3.544A  pdb=" N   VAL D   8 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 15
      removed outlier: 6.521A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 120 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   SER D  35 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   SER D  55 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ILE D  37 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 15
      removed outlier: 6.521A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 120 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR D 112 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8
      removed outlier: 3.603A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 13
      removed outlier: 3.539A  pdb=" N   LEU E  12 " --> pdb=" O   LYS E 104 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   TYR E  50 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 13
      removed outlier: 3.539A  pdb=" N   LEU E  12 " --> pdb=" O   LYS E 104 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR E  98 " --> pdb=" O   GLN E  91 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 118
    Processing sheet with id=AC1, first strand: chain 'F' and resid 27 through 29
      removed outlier: 4.019A  pdb=" N   PHE F 145 " --> pdb=" O   ILE F 169 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LYS F 171 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
      removed outlier: 10.325A  pdb=" N   VAL F 143 " --> pdb=" O   LYS F 171 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASP F 144 " --> pdb=" O   ALA F  61 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE F  88 " --> pdb=" O   VAL F  54 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL F  56 " --> pdb=" O   GLN F  86 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLN F  86 " --> pdb=" O   VAL F  56 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU F  58 " --> pdb=" O   ASN F  84 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASN F  84 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL F  60 " --> pdb=" O   ILE F  82 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   ILE F  82 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   PHE F  62 " --> pdb=" O   LEU F  80 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   LEU F  80 " --> pdb=" O   PHE F  62 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 27 through 29
      removed outlier: 4.019A  pdb=" N   PHE F 145 " --> pdb=" O   ILE F 169 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LYS F 171 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
      removed outlier: 10.325A  pdb=" N   VAL F 143 " --> pdb=" O   LYS F 171 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 184 through 190
      removed outlier: 3.880A  pdb=" N   SER F 203 " --> pdb=" O   ASN F 218 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASN F 223 " --> pdb=" O   SER F 267 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 208 through 209
      removed outlier: 3.637A  pdb=" N   VAL F 336 " --> pdb=" O   LEU F 328 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE F 342 " --> pdb=" O   TYR F 322 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TYR F 322 " --> pdb=" O   PHE F 342 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   LEU F 344 " --> pdb=" O   VAL F 320 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   VAL F 320 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ILE F 232 " --> pdb=" O   GLU F 258 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLU F 258 " --> pdb=" O   ILE F 232 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL F 234 " --> pdb=" O   GLN F 256 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLN F 256 " --> pdb=" O   VAL F 234 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL F 236 " --> pdb=" O   VAL F 254 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    999 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: 3.83

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3026
        1.34 -     1.46: 1903
        1.46 -     1.58: 4652
        1.58 -     1.69: 42
        1.69 -     1.81: 28
  Bond restraints: 9651
  Sorted by residual:
  bond pdb=" OG1 TPO H 354 "
       pdb=" P   TPO H 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" OG1 TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" O1P SEP H 345 "
       pdb=" P   SEP H 345 "
    ideal  model  delta    sigma   weight residual
    1.610  1.513  0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" O1P SEP G 343 "
       pdb=" P   SEP G 343 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" O2P SEP H 345 "
       pdb=" P   SEP H 345 "
    ideal  model  delta    sigma   weight residual
    1.610  1.515  0.095 2.00e-02 2.50e+03 2.27e+01
  ... (remaining 9646 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 12917
        2.54 -     5.08: 181
        5.08 -     7.61: 13
        7.61 -    10.15: 8
       10.15 -    12.69: 3
  Bond angle restraints: 13122
  Sorted by residual:
  angle pdb=" N   LEU F  49 "
        pdb=" CA  LEU F  49 "
        pdb=" C   LEU F  49 "
      ideal   model   delta    sigma   weight residual
     110.55   97.86   12.69 1.35e+00 5.49e-01 8.83e+01
  angle pdb=" N   LYS F  50 "
        pdb=" CA  LYS F  50 "
        pdb=" C   LYS F  50 "
      ideal   model   delta    sigma   weight residual
     112.12  103.01    9.11 1.34e+00 5.57e-01 4.62e+01
  angle pdb=" N   VAL A 315 "
        pdb=" CA  VAL A 315 "
        pdb=" C   VAL A 315 "
      ideal   model   delta    sigma   weight residual
     106.21  112.51   -6.30 1.07e+00 8.73e-01 3.47e+01
  angle pdb=" C   LEU A  49 "
        pdb=" N   LYS A  50 "
        pdb=" CA  LYS A  50 "
      ideal   model   delta    sigma   weight residual
     120.72  111.56    9.16 1.67e+00 3.59e-01 3.01e+01
  angle pdb=" N   PHE A 245 "
        pdb=" CA  PHE A 245 "
        pdb=" C   PHE A 245 "
      ideal   model   delta    sigma   weight residual
     114.75  108.37    6.38 1.26e+00 6.30e-01 2.56e+01
  ... (remaining 13117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 5348
       17.67 -    35.33: 363
       35.33 -    53.00: 67
       53.00 -    70.66: 13
       70.66 -    88.33: 15
  Dihedral angle restraints: 5806
    sinusoidal: 2297
      harmonic: 3509
  Sorted by residual:
  dihedral pdb=" CA  SER F  75 "
           pdb=" C   SER F  75 "
           pdb=" N   PHE F  76 "
           pdb=" CA  PHE F  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.85   20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  LEU F 244 "
           pdb=" C   LEU F 244 "
           pdb=" N   PHE F 245 "
           pdb=" CA  PHE F 245 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.87   19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  SER A  75 "
           pdb=" C   SER A  75 "
           pdb=" N   PHE A  76 "
           pdb=" CA  PHE A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 5803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1284
       0.070 -    0.140: 173
       0.140 -    0.210: 7
       0.210 -    0.279: 1
       0.279 -    0.349: 2
  Chirality restraints: 1467
  Sorted by residual:
  chirality pdb=" CA  LEU A  49 "
            pdb=" N   LEU A  49 "
            pdb=" C   LEU A  49 "
            pdb=" CB  LEU A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  LEU F  49 "
            pdb=" N   LEU F  49 "
            pdb=" C   LEU F  49 "
            pdb=" CB  LEU F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CA  LYS F  50 "
            pdb=" N   LYS F  50 "
            pdb=" C   LYS F  50 "
            pdb=" CB  LYS F  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1464 not shown)

  Planarity restraints: 1672
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F  48 "   -0.018 2.00e-02 2.50e+03   3.77e-02 1.42e+01
        pdb=" C   TYR F  48 "    0.065 2.00e-02 2.50e+03
        pdb=" O   TYR F  48 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU F  49 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS F 350 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.06e+00
        pdb=" C   HIS F 350 "    0.035 2.00e-02 2.50e+03
        pdb=" O   HIS F 350 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASP F 351 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  48 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   TYR A  48 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   TYR A  48 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  49 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1669 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1311
        2.76 -     3.30: 8412
        3.30 -     3.83: 14735
        3.83 -     4.37: 17043
        4.37 -     4.90: 31706
  Nonbonded interactions: 73207
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 205 "
            pdb=" OH  TYR A 209 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OD1 ASP F 205 "
            pdb=" OH  TYR F 209 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OD2 ASP F 261 "
            pdb=" OH  TYR F 273 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OD2 ASP A 261 "
            pdb=" OH  TYR A 273 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" NZ  LYS F 293 "
            pdb=" OG1 THR F 299 "
     model   vdw
     2.277 3.120
  ... (remaining 73202 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and resid 5 through 121)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'E' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 65 or (resid 66 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 67 through 107))
}
ncs_group {
  reference = chain 'G'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.990
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
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      :  0.005   0.109   9655  Z= 0.265
  Angle     :  0.717  12.689  13130  Z= 0.399
  Chirality :  0.046   0.349   1467
  Planarity :  0.004   0.045   1672
  Dihedral  : 13.272  88.326   3536
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  0.59 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1163
  helix:  2.76 (0.69), residues: 52
  sheet:  0.66 (0.23), residues: 521
  loop : -0.54 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A 346 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.010   0.001   TYR E  50 
 ARG   0.005   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22099 (  356)
  hydrogen bonds       : angle       8.95165 (  999)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       0.28061 (    8)
  covalent geometry    : bond        0.00509 ( 9651)
  covalent geometry    : angle       0.71767 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 1.136 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.5562 (m90) cc_final: 0.5345 (m170)
REVERT: B   76 ASP cc_start: 0.7148 (t0) cc_final: 0.6899 (t0)
REVERT: D   76 ASP cc_start: 0.7074 (t0) cc_final: 0.6860 (t0)
REVERT: F   52 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4918 (mtp180)
REVERT: F  351 ASP cc_start: 0.4956 (OUTLIER) cc_final: 0.4301 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 131
  average time/residue: 0.2684
  time to fit residues: 48.9351
Evaluate side-chains
  106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   52 ARG
Chi-restraints excluded: chain F residue  351 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
A 160 HIS
B  87 ASN
F 112 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.158944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125231 restraints weight = 12927.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.80
r_work: 0.3271 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9655  Z= 0.190
  Angle     :  0.608  10.815  13130  Z= 0.315
  Chirality :  0.046   0.159   1467
  Planarity :  0.005   0.047   1672
  Dihedral  :  8.439  79.438   1377
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  6.44 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1163
  helix:  2.73 (0.69), residues: 54
  sheet:  0.60 (0.23), residues: 528
  loop : -0.57 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  50 
 HIS   0.007   0.001   HIS F 199 
 PHE   0.013   0.002   PHE A 117 
 TYR   0.014   0.002   TYR F 273 
 ARG   0.004   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  356)
  hydrogen bonds       : angle       6.02362 (  999)
  SS BOND              : bond        0.00538 (    4)
  SS BOND              : angle       0.41645 (    8)
  covalent geometry    : bond        0.00447 ( 9651)
  covalent geometry    : angle       0.60774 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.211 
Fit side-chains
REVERT: A  351 ASP cc_start: 0.6129 (OUTLIER) cc_final: 0.5809 (t70)
REVERT: E   25 ARG cc_start: 0.8242 (tpt170) cc_final: 0.7952 (tpp-160)
REVERT: F  351 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.4916 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 112
  average time/residue: 0.2350
  time to fit residues: 36.6197
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue    4 GLN
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  306 ILE
Chi-restraints excluded: chain F residue  351 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0970
   chunk 107 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 58 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0870
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
F 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.161738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.129130 restraints weight = 12969.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.79
r_work: 0.3317 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9655  Z= 0.102
  Angle     :  0.522  11.259  13130  Z= 0.268
  Chirality :  0.043   0.139   1467
  Planarity :  0.004   0.044   1672
  Dihedral  :  7.866  77.859   1367
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  8.29 %
    Favored  : 90.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1163
  helix:  2.84 (0.69), residues: 54
  sheet:  0.61 (0.22), residues: 550
  loop : -0.29 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  36 
 HIS   0.005   0.001   HIS F 199 
 PHE   0.011   0.001   PHE A 116 
 TYR   0.011   0.001   TYR F 273 
 ARG   0.003   0.000   ARG F  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03077 (  356)
  hydrogen bonds       : angle       5.36514 (  999)
  SS BOND              : bond        0.00380 (    4)
  SS BOND              : angle       0.26454 (    8)
  covalent geometry    : bond        0.00231 ( 9651)
  covalent geometry    : angle       0.52220 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.131 
Fit side-chains
REVERT: A  193 MET cc_start: 0.6081 (ppp) cc_final: 0.5744 (ppp)
REVERT: A  351 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.6033 (t70)
REVERT: C   25 ARG cc_start: 0.8171 (tpt170) cc_final: 0.7959 (tpp-160)
REVERT: E   25 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7967 (tpp-160)
REVERT: F  351 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5078 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 112
  average time/residue: 0.2195
  time to fit residues: 34.9346
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  260 ASP
Chi-restraints excluded: chain F residue  351 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0040
   chunk 65 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 115 optimal weight:    6.9990
   overall best weight:    0.8994

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
B  87 ASN
F 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.152479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.122855 restraints weight = 12617.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.27
r_work: 0.3249 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9655  Z= 0.152
  Angle     :  0.544  10.872  13130  Z= 0.279
  Chirality :  0.044   0.151   1467
  Planarity :  0.004   0.045   1672
  Dihedral  :  7.800  77.123   1367
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  9.66 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1163
  helix:  2.81 (0.70), residues: 54
  sheet:  0.61 (0.22), residues: 550
  loop : -0.35 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  50 
 HIS   0.006   0.001   HIS F 199 
 PHE   0.012   0.002   PHE A 116 
 TYR   0.011   0.001   TYR C  92 
 ARG   0.002   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03056 (  356)
  hydrogen bonds       : angle       5.24840 (  999)
  SS BOND              : bond        0.00487 (    4)
  SS BOND              : angle       0.17562 (    8)
  covalent geometry    : bond        0.00359 ( 9651)
  covalent geometry    : angle       0.54446 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 1.033 
Fit side-chains
REVERT: A  351 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5792 (t70)
REVERT: F  230 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7788 (mmmm)
REVERT: F  351 ASP cc_start: 0.6338 (OUTLIER) cc_final: 0.5396 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1994
  time to fit residues: 32.4577
Evaluate side-chains
  115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue    4 GLN
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  260 ASP
Chi-restraints excluded: chain F residue  351 ASP
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0170
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.1424

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
F 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.151012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121089 restraints weight = 12700.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.32
r_work: 0.3212 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9655  Z= 0.181
  Angle     :  0.569  10.802  13130  Z= 0.291
  Chirality :  0.044   0.156   1467
  Planarity :  0.004   0.046   1672
  Dihedral  :  7.839  76.390   1367
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.51 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1163
  helix:  2.80 (0.70), residues: 54
  sheet:  0.54 (0.22), residues: 550
  loop : -0.43 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  50 
 HIS   0.007   0.001   HIS A 199 
 PHE   0.013   0.002   PHE F 117 
 TYR   0.013   0.002   TYR B  98 
 ARG   0.005   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03118 (  356)
  hydrogen bonds       : angle       5.22940 (  999)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       0.19174 (    8)
  covalent geometry    : bond        0.00430 ( 9651)
  covalent geometry    : angle       0.56905 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 1.429 
Fit side-chains
REVERT: A  351 ASP cc_start: 0.6256 (OUTLIER) cc_final: 0.5908 (t70)
REVERT: F  230 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7825 (mmmm)
REVERT: F  351 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.5878 (t0)
  outliers start: 26
  outliers final: 19
  residues processed: 108
  average time/residue: 0.2270
  time to fit residues: 34.6794
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue    4 GLN
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  351 ASP
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
F 112 HIS
F 211 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.150756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.121329 restraints weight = 12576.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.25
r_work: 0.3215 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9655  Z= 0.172
  Angle     :  0.557  10.388  13130  Z= 0.286
  Chirality :  0.044   0.154   1467
  Planarity :  0.004   0.046   1672
  Dihedral  :  7.751  75.600   1367
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.10 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1163
  helix:  2.76 (0.69), residues: 54
  sheet:  0.58 (0.22), residues: 552
  loop : -0.47 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  50 
 HIS   0.007   0.001   HIS A 199 
 PHE   0.014   0.002   PHE A 117 
 TYR   0.012   0.001   TYR B  98 
 ARG   0.005   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  356)
  hydrogen bonds       : angle       5.16718 (  999)
  SS BOND              : bond        0.00488 (    4)
  SS BOND              : angle       0.20278 (    8)
  covalent geometry    : bond        0.00410 ( 9651)
  covalent geometry    : angle       0.55764 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.058 
Fit side-chains
REVERT: F  230 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7807 (mmmm)
  outliers start: 21
  outliers final: 18
  residues processed: 108
  average time/residue: 0.2176
  time to fit residues: 33.6787
Evaluate side-chains
  111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
F 112 HIS

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 = 0.148401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.118302 restraints weight = 12716.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.29
r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   9655  Z= 0.281
  Angle     :  0.657  11.339  13130  Z= 0.337
  Chirality :  0.047   0.173   1467
  Planarity :  0.005   0.049   1672
  Dihedral  :  7.807  75.676   1363
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.39 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1163
  helix:  2.43 (0.66), residues: 54
  sheet:  0.41 (0.22), residues: 538
  loop : -0.56 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  50 
 HIS   0.010   0.001   HIS A 199 
 PHE   0.017   0.002   PHE F 117 
 TYR   0.018   0.002   TYR E  92 
 ARG   0.004   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  356)
  hydrogen bonds       : angle       5.53354 (  999)
  SS BOND              : bond        0.00575 (    4)
  SS BOND              : angle       0.26761 (    8)
  covalent geometry    : bond        0.00669 ( 9651)
  covalent geometry    : angle       0.65732 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 1.094 
Fit side-chains
REVERT: F  230 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7879 (mmmm)
  outliers start: 23
  outliers final: 21
  residues processed: 112
  average time/residue: 0.2135
  time to fit residues: 34.1185
Evaluate side-chains
  120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  111 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0980
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
F 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.151496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121928 restraints weight = 12724.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.26
r_work: 0.3230 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9655  Z= 0.123
  Angle     :  0.533   9.918  13130  Z= 0.273
  Chirality :  0.043   0.138   1467
  Planarity :  0.004   0.049   1672
  Dihedral  :  7.524  74.361   1363
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.85 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1163
  helix:  2.73 (0.69), residues: 54
  sheet:  0.52 (0.23), residues: 540
  loop : -0.49 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  50 
 HIS   0.005   0.001   HIS F 199 
 PHE   0.011   0.001   PHE A 116 
 TYR   0.009   0.001   TYR C  50 
 ARG   0.002   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02760 (  356)
  hydrogen bonds       : angle       5.04292 (  999)
  SS BOND              : bond        0.00397 (    4)
  SS BOND              : angle       0.33089 (    8)
  covalent geometry    : bond        0.00288 ( 9651)
  covalent geometry    : angle       0.53324 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.067 
Fit side-chains
REVERT: B    5 VAL cc_start: 0.8038 (t) cc_final: 0.7706 (p)
REVERT: D   92 GLU cc_start: 0.7665 (mp0) cc_final: 0.7446 (mp0)
REVERT: F  230 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7849 (mmmm)
  outliers start: 16
  outliers final: 14
  residues processed: 106
  average time/residue: 0.2294
  time to fit residues: 34.0425
Evaluate side-chains
  109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0060
   chunk 91 optimal weight:    0.0570
   overall best weight:    0.5516

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
F 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.152279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122466 restraints weight = 12586.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.22
r_work: 0.3236 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9655  Z= 0.115
  Angle     :  0.521   9.349  13130  Z= 0.266
  Chirality :  0.043   0.142   1467
  Planarity :  0.004   0.046   1672
  Dihedral  :  7.247  73.167   1363
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.46 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1163
  helix:  2.87 (0.69), residues: 54
  sheet:  0.64 (0.23), residues: 540
  loop : -0.41 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  36 
 HIS   0.005   0.001   HIS F 199 
 PHE   0.012   0.001   PHE F 116 
 TYR   0.012   0.001   TYR F  48 
 ARG   0.003   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02615 (  356)
  hydrogen bonds       : angle       4.87793 (  999)
  SS BOND              : bond        0.00410 (    4)
  SS BOND              : angle       0.27771 (    8)
  covalent geometry    : bond        0.00271 ( 9651)
  covalent geometry    : angle       0.52110 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.034 
Fit side-chains
REVERT: B    5 VAL cc_start: 0.7989 (t) cc_final: 0.7679 (p)
REVERT: F   51 ASP cc_start: 0.5902 (OUTLIER) cc_final: 0.5641 (p0)
REVERT: F  230 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7784 (mmmm)
  outliers start: 21
  outliers final: 19
  residues processed: 107
  average time/residue: 0.2154
  time to fit residues: 32.7749
Evaluate side-chains
  110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  329 VAL
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 115 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
F 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.151656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.122026 restraints weight = 12706.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.48
r_work: 0.3215 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9655  Z= 0.139
  Angle     :  0.548   9.617  13130  Z= 0.276
  Chirality :  0.043   0.163   1467
  Planarity :  0.004   0.046   1672
  Dihedral  :  7.226  72.626   1363
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.66 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1163
  helix:  2.87 (0.69), residues: 54
  sheet:  0.54 (0.22), residues: 558
  loop : -0.38 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  50 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.012   0.001   PHE A 116 
 TYR   0.011   0.001   TYR B  98 
 ARG   0.003   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02712 (  356)
  hydrogen bonds       : angle       4.90949 (  999)
  SS BOND              : bond        0.00436 (    4)
  SS BOND              : angle       0.30279 (    8)
  covalent geometry    : bond        0.00331 ( 9651)
  covalent geometry    : angle       0.54854 (13122)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 1.041 
Fit side-chains
REVERT: B    5 VAL cc_start: 0.8002 (t) cc_final: 0.7689 (p)
REVERT: F   51 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5643 (p0)
REVERT: F  230 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7777 (mmmm)
  outliers start: 19
  outliers final: 18
  residues processed: 103
  average time/residue: 0.2107
  time to fit residues: 30.8353
Evaluate side-chains
  109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue  101 GLN
Chi-restraints excluded: chain D residue   93 ASP
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  101 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue  190 HIS
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  329 VAL
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain G residue  352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 47 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0670
   chunk 59 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0000
   overall best weight:    0.4722

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
** C 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 ASN
** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.153127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123144 restraints weight = 12598.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.21
r_work: 0.3272 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9655  Z= 0.106
  Angle     :  0.524   9.224  13130  Z= 0.263
  Chirality :  0.042   0.135   1467
  Planarity :  0.004   0.046   1672
  Dihedral  :  7.014  71.512   1363
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.07 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1163
  helix:  2.93 (0.69), residues: 54
  sheet:  0.63 (0.22), residues: 556
  loop : -0.33 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  36 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.011   0.001   PHE A 116 
 TYR   0.009   0.001   TYR C  50 
 ARG   0.002   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02489 (  356)
  hydrogen bonds       : angle       4.74026 (  999)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       0.30238 (    8)
  covalent geometry    : bond        0.00251 ( 9651)
  covalent geometry    : angle       0.52401 (13122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4651.28 seconds
wall clock time: 82 minutes 39.52 seconds (4959.52 seconds total)