Starting phenix.real_space_refine
on Fri May 16 00:01:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyb_29563/05_2025/8fyb_29563.cif"
  }
  resolution = 3.1
  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=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 571 atoms to isotropic.
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     135      5.49       5
     S      32      5.16       5
     C    8099      2.51       5
     N    2441      2.21       5
     O    2779      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13486
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 737
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "C"
      Number of atoms: 2414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2414
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 13, 'TRANS': 295}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "F"
      Number of atoms: 2188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2188
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "G"
      Number of atoms: 1089
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 52, 1067
          Classifications: {'DNA': 52}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 51}
      Conformer: "B"
        Number of residues, atoms: 52, 1067
          Classifications: {'DNA': 52}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 51}
          bond proxies already assigned to first conformer: 1170
    Chain: "H"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 632
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "J"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 742
          Classifications: {'DNA': 36}
          Link IDs: {'rna3p': 35}
    Chain: "I"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 348
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DG G  29 " occ=0.50
      ... (42 atoms not shown)
      pdb=" C4 B DG G  29 " occ=0.50
  Time building chain proxies: 8.96, per 1000 atoms: 0.66
  Number of scatterers: 13486
  At special positions: 0
  Unit cell: (123.765, 97.005, 163.905, 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      32     16.00
     P     135     15.00
     O    2779      8.00
     N    2441      7.00
     C    8099      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.92
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2510

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      51.5% alpha, 14.4% beta
      33 base pairs and 109 stacking pairs defined.
    Time for finding SS restraints: 4.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 23
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'B' and resid 68 through 77
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 3.838A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 130
    Processing helix  chain 'B' and resid 139 through 162
    Processing helix  chain 'B' and resid 180 through 205
      removed outlier: 3.591A  pdb=" N   LEU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 231
      removed outlier: 4.028A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   TYR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ALA B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 250 through 263
      removed outlier: 3.535A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 4.084A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 53
      No H-bonds generated for 'chain 'C' and resid 51 through 53'
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.643A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.830A  pdb=" N   LYS C 107 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
    Processing helix  chain 'C' and resid 139 through 163
    Processing helix  chain 'C' and resid 180 through 204
      removed outlier: 3.799A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 193 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.687A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 267
    Processing helix  chain 'C' and resid 267 through 280
      removed outlier: 3.688A  pdb=" N   LEU C 280 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 51
    Processing helix  chain 'E' and resid 51 through 55
      removed outlier: 3.790A  pdb=" N   MET E  54 " --> pdb=" O   PRO E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 77
    Processing helix  chain 'E' and resid 86 through 89
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 4.379A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 130
    Processing helix  chain 'E' and resid 139 through 162
    Processing helix  chain 'E' and resid 180 through 205
    Processing helix  chain 'E' and resid 219 through 231
      removed outlier: 4.771A  pdb=" N   LEU E 228 " --> pdb=" O   ASP E 224 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR E 229 " --> pdb=" O   VAL E 225 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 244
    Processing helix  chain 'E' and resid 250 through 266
      removed outlier: 4.022A  pdb=" N   LEU E 254 " --> pdb=" O   ASP E 250 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY E 266 " --> pdb=" O   ALA E 262 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
      removed outlier: 3.854A  pdb=" N   LYS E 270 " --> pdb=" O   GLY E 266 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E 280 " --> pdb=" O   LEU E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'E' and resid 304 through 306
      No H-bonds generated for 'chain 'E' and resid 304 through 306'
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 67 through 77
      removed outlier: 3.703A  pdb=" N   VAL F  71 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.635A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
    Processing helix  chain 'F' and resid 139 through 163
    Processing helix  chain 'F' and resid 180 through 205
      removed outlier: 3.681A  pdb=" N   ALA F 192 " --> pdb=" O   ALA F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 244
      removed outlier: 3.767A  pdb=" N   TYR F 229 " --> pdb=" O   VAL F 225 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   GLU F 232 " --> pdb=" O   LEU F 228 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL F 235 " --> pdb=" O   ALA F 231 " (cutoff:3.500A)
      Proline residue:  F 236  - end of helix
    Processing helix  chain 'F' and resid 250 through 267
    Processing helix  chain 'F' and resid 267 through 280
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.939A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   MET A   3 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 5.717A  pdb=" N   ILE A  88 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG F  49 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ALA E  30 " --> pdb=" O   ASP E  65 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   SER E  67 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ILE E  32 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94
      removed outlier: 6.608A  pdb=" N   TRP B  83 " --> pdb=" O   TYR B  92 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   SER B  94 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA B  22 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40
      removed outlier: 6.988A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   ILE B  32 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48
    Processing sheet with id=AA6, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 27
      removed outlier: 6.395A  pdb=" N   THR C  23 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   LEU C  59 " --> pdb=" O   THR C  23 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA C  80 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR C  91 " --> pdb=" O   TRP C  83 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLY C  85 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   VAL C  89 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
      removed outlier: 5.806A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL D  32 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA D  27 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   MET D   3 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA D  61 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94
      removed outlier: 6.049A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR E  26 " --> pdb=" O   LEU E 293 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 47 through 49
      removed outlier: 4.078A  pdb=" N   ASN E 308 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 27
      removed outlier: 6.463A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR F  91 " --> pdb=" O   TRP F  83 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLY F  85 " --> pdb=" O   VAL F  89 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   VAL F  89 " --> pdb=" O   GLY F  85 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      78 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      110 stacking parallelities
  Total time for adding SS restraints: 4.11

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3437
        1.33 -     1.45: 3290
        1.45 -     1.57: 6968
        1.57 -     1.69: 269
        1.69 -     1.82: 62
  Bond restraints: 14026
  Sorted by residual:
  bond pdb=" CA  TRP E 166 "
       pdb=" C   TRP E 166 "
    ideal  model  delta    sigma   weight residual
    1.528  1.506  0.022 1.18e-02 7.18e+03 3.38e+00
  bond pdb=" CA  ARG E 169 "
       pdb=" C   ARG E 169 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.022 1.34e-02 5.57e+03 2.62e+00
  bond pdb=" C3'  DG G   8 "
       pdb=" O3'  DG G   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" CA  VAL E 170 "
       pdb=" C   VAL E 170 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.27e-02 6.20e+03 1.77e+00
  bond pdb=" CA  TYR E 171 "
       pdb=" C   TYR E 171 "
    ideal  model  delta    sigma   weight residual
    1.525  1.508  0.016 1.25e-02 6.40e+03 1.69e+00
  ... (remaining 14021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 19117
        1.82 -     3.64: 414
        3.64 -     5.47: 34
        5.47 -     7.29: 6
        7.29 -     9.11: 2
  Bond angle restraints: 19573
  Sorted by residual:
  angle pdb=" N   LYS E 167 "
        pdb=" CA  LYS E 167 "
        pdb=" C   LYS E 167 "
      ideal   model   delta    sigma   weight residual
     110.53  102.86    7.67 1.29e+00 6.01e-01 3.54e+01
  angle pdb=" N   LYS E 168 "
        pdb=" CA  LYS E 168 "
        pdb=" C   LYS E 168 "
      ideal   model   delta    sigma   weight residual
     110.35  117.00   -6.65 1.36e+00 5.41e-01 2.39e+01
  angle pdb=" N   TRP E 166 "
        pdb=" CA  TRP E 166 "
        pdb=" C   TRP E 166 "
      ideal   model   delta    sigma   weight residual
     107.37  116.48   -9.11 2.07e+00 2.33e-01 1.94e+01
  angle pdb=" CA  PRO E 165 "
        pdb=" C   PRO E 165 "
        pdb=" N   TRP E 166 "
      ideal   model   delta    sigma   weight residual
     114.75  119.47   -4.72 1.45e+00 4.76e-01 1.06e+01
  angle pdb=" CA  PRO E 165 "
        pdb=" C   PRO E 165 "
        pdb=" O   PRO E 165 "
      ideal   model   delta    sigma   weight residual
     122.31  117.91    4.40 1.41e+00 5.03e-01 9.75e+00
  ... (remaining 19568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 7454
       35.90 -    71.81: 584
       71.81 -   107.71: 17
      107.71 -   143.62: 3
      143.62 -   179.52: 4
  Dihedral angle restraints: 8062
    sinusoidal: 4145
      harmonic: 3917
  Sorted by residual:
  dihedral pdb=" C4'  DA J  30 "
           pdb=" C3'  DA J  30 "
           pdb=" O3'  DA J  30 "
           pdb=" P    DA J  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.52 -179.52     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  25 "
           pdb=" C3'  DG J  25 "
           pdb=" O3'  DG J  25 "
           pdb=" P    DC J  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.59  178.41     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J  31 "
           pdb=" C3'  DA J  31 "
           pdb=" O3'  DA J  31 "
           pdb=" P    DA J  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.10 -178.10     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 8059 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1624
       0.039 -    0.079: 430
       0.079 -    0.118: 115
       0.118 -    0.157: 24
       0.157 -    0.196: 2
  Chirality restraints: 2195
  Sorted by residual:
  chirality pdb=" CA  LYS E 168 "
            pdb=" N   LYS E 168 "
            pdb=" C   LYS E 168 "
            pdb=" CB  LYS E 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality pdb=" CA  TRP E 166 "
            pdb=" N   TRP E 166 "
            pdb=" C   TRP E 166 "
            pdb=" CB  TRP E 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  VAL B 303 "
            pdb=" N   VAL B 303 "
            pdb=" C   VAL B 303 "
            pdb=" CB  VAL B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 2192 not shown)

  Planarity restraints: 2042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  50 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO B  51 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  51 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  51 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 291 "   -0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO E 292 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 292 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 292 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 160 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   LYS E 160 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS E 160 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS E 161 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2039 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1663
        2.75 -     3.29: 12870
        3.29 -     3.82: 25087
        3.82 -     4.36: 29445
        4.36 -     4.90: 47320
  Nonbonded interactions: 116385
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 223 "
            pdb=" N2   DG G  27 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" NH2 ARG E 124 "
            pdb=" OE1 GLU E 281 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OH  TYR B 126 "
            pdb=" O4   DT H  29 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" NH2 ARG B 256 "
            pdb=" OP1  DT H  23 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OH  TYR E  92 "
            pdb=" OP2  DC G  24 "
     model   vdw
     2.254 3.040
  ... (remaining 116380 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 'D' and resid 1 through 92)
}
ncs_group {
  reference = (chain 'B' and resid 20 through 282)
  selection = (chain 'C' and resid 20 through 282)
  selection = (chain 'E' and resid 20 through 282)
  selection = (chain 'F' and resid 20 through 282)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     33.800
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  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:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14026  Z= 0.194
  Angle     :  0.598   9.109  19573  Z= 0.341
  Chirality :  0.039   0.196   2195
  Planarity :  0.004   0.049   2042
  Dihedral  : 20.880 179.521   5552
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.18 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.63 (0.23), residues: 1347
  helix:  1.66 (0.20), residues: 635
  sheet: -0.29 (0.37), residues: 214
  loop : -0.85 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 166 
 HIS   0.012   0.001   HIS B 198 
 PHE   0.017   0.002   PHE A  35 
 TYR   0.015   0.002   TYR E 162 
 ARG   0.007   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14203 (  655)
  hydrogen bonds       : angle       6.27044 ( 1812)
  covalent geometry    : bond        0.00434 (14026)
  covalent geometry    : angle       0.59819 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 294
  time to evaluate  : 1.347 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7611 (ttt) cc_final: 0.6837 (ttt)
REVERT: B  175 ASP cc_start: 0.7927 (t0) cc_final: 0.7550 (t70)
REVERT: B  275 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (m-30)
REVERT: B  289 GLU cc_start: 0.7826 (tp30) cc_final: 0.7613 (tp30)
REVERT: C  162 TYR cc_start: 0.8341 (m-80) cc_final: 0.7963 (m-80)
REVERT: C  233 ILE cc_start: 0.7577 (mt) cc_final: 0.7260 (mt)
REVERT: C  274 LYS cc_start: 0.8113 (tppt) cc_final: 0.7883 (tptp)
REVERT: E   72 GLU cc_start: 0.7249 (tp30) cc_final: 0.6892 (mm-30)
REVERT: E   76 ASP cc_start: 0.6861 (m-30) cc_final: 0.6636 (m-30)
REVERT: E  154 LYS cc_start: 0.7294 (tppp) cc_final: 0.6566 (tppt)
REVERT: E  172 ASN cc_start: 0.8074 (t0) cc_final: 0.7646 (t0)
REVERT: E  175 ASP cc_start: 0.7559 (t70) cc_final: 0.7091 (m-30)
REVERT: E  193 LEU cc_start: 0.8391 (tp) cc_final: 0.8148 (tp)
REVERT: E  272 MET cc_start: 0.7782 (mtt) cc_final: 0.7550 (mtp)
REVERT: F  101 SER cc_start: 0.8939 (t) cc_final: 0.8702 (p)
REVERT: F  275 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 295
  average time/residue: 0.3034
  time to fit residues: 122.4315
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    8.9990
   chunk 110 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 37 optimal weight:    4.9990
   chunk 74 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
C  33 ASN
E 183 ASN
F  33 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.179502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116885 restraints weight = 17024.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.35
r_work: 0.3271 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14026  Z= 0.197
  Angle     :  0.608   6.663  19573  Z= 0.341
  Chirality :  0.042   0.166   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.232 177.877   3008
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.63 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.66 (0.23), residues: 1347
  helix:  1.72 (0.20), residues: 641
  sheet: -0.46 (0.36), residues: 216
  loop : -0.82 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 296 
 HIS   0.009   0.001   HIS E  29 
 PHE   0.009   0.001   PHE E 239 
 TYR   0.013   0.002   TYR E 223 
 ARG   0.006   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04554 (  655)
  hydrogen bonds       : angle       4.30341 ( 1812)
  covalent geometry    : bond        0.00454 (14026)
  covalent geometry    : angle       0.60777 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 1.348 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7953 (ttt) cc_final: 0.7288 (ttt)
REVERT: A   45 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.7130 (mtp85)
REVERT: A   73 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7542 (tp30)
REVERT: B  138 LEU cc_start: 0.8573 (mp) cc_final: 0.8319 (tp)
REVERT: B  289 GLU cc_start: 0.8212 (tp30) cc_final: 0.7772 (tp30)
REVERT: C  156 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7265 (ptt90)
REVERT: C  162 TYR cc_start: 0.8303 (m-80) cc_final: 0.7961 (m-80)
REVERT: C  253 GLN cc_start: 0.8037 (tt0) cc_final: 0.7820 (mt0)
REVERT: D   51 MET cc_start: 0.8452 (ptt) cc_final: 0.8225 (ptt)
REVERT: D   78 SER cc_start: 0.8238 (m) cc_final: 0.7935 (t)
REVERT: E   72 GLU cc_start: 0.7637 (tp30) cc_final: 0.6625 (tp30)
REVERT: E   76 ASP cc_start: 0.7057 (m-30) cc_final: 0.6564 (m-30)
REVERT: E  155 TYR cc_start: 0.7297 (m-10) cc_final: 0.6985 (m-80)
REVERT: E  172 ASN cc_start: 0.7958 (t0) cc_final: 0.7628 (t0)
REVERT: F  101 SER cc_start: 0.9159 (t) cc_final: 0.8812 (p)
REVERT: F  275 ASP cc_start: 0.8239 (m-30) cc_final: 0.7830 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 214
  average time/residue: 0.2909
  time to fit residues: 86.5819
Evaluate side-chains
  190 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 180
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  310 SER
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  237 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 134 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
E 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.180534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118269 restraints weight = 18769.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.38
r_work: 0.3265 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.165
  Angle     :  0.558   6.478  19573  Z= 0.314
  Chirality :  0.040   0.138   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.314 177.123   3008
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.51 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.75 (0.23), residues: 1347
  helix:  1.84 (0.20), residues: 641
  sheet: -0.47 (0.36), residues: 210
  loop : -0.81 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 296 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.010   0.001   PHE A  89 
 TYR   0.018   0.001   TYR E 223 
 ARG   0.007   0.001   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  655)
  hydrogen bonds       : angle       3.98574 ( 1812)
  covalent geometry    : bond        0.00377 (14026)
  covalent geometry    : angle       0.55800 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 1.345 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7797 (ttt) cc_final: 0.7060 (ttt)
REVERT: A   45 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7238 (mtp85)
REVERT: A   73 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7624 (tp30)
REVERT: B  138 LEU cc_start: 0.8612 (mp) cc_final: 0.8379 (tp)
REVERT: B  281 GLU cc_start: 0.8122 (mp0) cc_final: 0.7454 (mp0)
REVERT: C   49 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7430 (mtp180)
REVERT: C  156 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7178 (ptt90)
REVERT: C  253 GLN cc_start: 0.7975 (tt0) cc_final: 0.7685 (mt0)
REVERT: C  300 GLU cc_start: 0.7910 (tp30) cc_final: 0.7605 (tp30)
REVERT: D   58 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8200 (ttt)
REVERT: D   78 SER cc_start: 0.8228 (m) cc_final: 0.7875 (t)
REVERT: E   72 GLU cc_start: 0.7595 (tp30) cc_final: 0.6694 (tm-30)
REVERT: E   76 ASP cc_start: 0.7224 (m-30) cc_final: 0.6627 (m-30)
REVERT: E  155 TYR cc_start: 0.7334 (m-10) cc_final: 0.7016 (m-80)
REVERT: E  172 ASN cc_start: 0.8015 (t0) cc_final: 0.7614 (t0)
REVERT: E  193 LEU cc_start: 0.8242 (tp) cc_final: 0.7802 (tp)
REVERT: F  101 SER cc_start: 0.9164 (t) cc_final: 0.8768 (p)
REVERT: F  104 PHE cc_start: 0.8632 (m-10) cc_final: 0.8399 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 211
  average time/residue: 0.2980
  time to fit residues: 88.6375
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  310 SER
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0470
   chunk 91 optimal weight:    6.9990
   chunk 116 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 108 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 129 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.3282

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

Flipped N/Q/H residues before XYZ refinement:
E 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.178434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116344 restraints weight = 17092.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.39
r_work: 0.3227 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14026  Z= 0.195
  Angle     :  0.573   6.454  19573  Z= 0.321
  Chirality :  0.041   0.178   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.411 176.658   3008
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.41 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.73 (0.23), residues: 1347
  helix:  1.86 (0.20), residues: 639
  sheet: -0.50 (0.37), residues: 200
  loop : -0.86 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 166 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.011   0.001   PHE A  89 
 TYR   0.012   0.001   TYR F 126 
 ARG   0.007   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  655)
  hydrogen bonds       : angle       3.99576 ( 1812)
  covalent geometry    : bond        0.00453 (14026)
  covalent geometry    : angle       0.57305 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 1.200 
Fit side-chains
REVERT: A    3 MET cc_start: 0.8100 (ttt) cc_final: 0.7401 (ttt)
REVERT: A   45 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7349 (mtp85)
REVERT: B  130 PHE cc_start: 0.7256 (m-80) cc_final: 0.6775 (m-80)
REVERT: C   49 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7758 (mtp85)
REVERT: C  253 GLN cc_start: 0.8081 (tt0) cc_final: 0.7790 (mt0)
REVERT: D   78 SER cc_start: 0.8335 (m) cc_final: 0.8004 (t)
REVERT: E   72 GLU cc_start: 0.7658 (tp30) cc_final: 0.6763 (tm-30)
REVERT: E   76 ASP cc_start: 0.7274 (m-30) cc_final: 0.6692 (m-30)
REVERT: E  155 TYR cc_start: 0.7517 (m-10) cc_final: 0.7249 (m-80)
REVERT: E  172 ASN cc_start: 0.8103 (t0) cc_final: 0.7698 (t0)
REVERT: F  101 SER cc_start: 0.9138 (t) cc_final: 0.8768 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 196
  average time/residue: 0.2757
  time to fit residues: 75.7172
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  272 MET
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 135 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 108 optimal weight:    0.3980
   chunk 51 optimal weight:    0.0870
   chunk 121 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.8760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.179873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117556 restraints weight = 17362.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.38
r_work: 0.3271 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.162
  Angle     :  0.553   6.464  19573  Z= 0.311
  Chirality :  0.040   0.174   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.441 175.587   3008
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.21 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.80 (0.23), residues: 1347
  helix:  1.96 (0.20), residues: 640
  sheet: -0.42 (0.37), residues: 198
  loop : -0.92 (0.25), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 166 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.012   0.001   PHE A  89 
 TYR   0.012   0.001   TYR F 229 
 ARG   0.006   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  655)
  hydrogen bonds       : angle       3.85770 ( 1812)
  covalent geometry    : bond        0.00370 (14026)
  covalent geometry    : angle       0.55304 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 1.369 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7228 (mtp85)
REVERT: B  130 PHE cc_start: 0.7137 (m-80) cc_final: 0.6668 (m-80)
REVERT: C  253 GLN cc_start: 0.8021 (tt0) cc_final: 0.7529 (mm-40)
REVERT: D   51 MET cc_start: 0.8587 (ptt) cc_final: 0.8122 (ptt)
REVERT: D   78 SER cc_start: 0.8240 (m) cc_final: 0.7924 (t)
REVERT: E   72 GLU cc_start: 0.7570 (tp30) cc_final: 0.7334 (tm-30)
REVERT: E  124 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.6775 (ttp-170)
REVERT: E  172 ASN cc_start: 0.8016 (t0) cc_final: 0.7618 (t0)
REVERT: F  101 SER cc_start: 0.9117 (t) cc_final: 0.8722 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 199
  average time/residue: 0.2850
  time to fit residues: 79.6697
Evaluate side-chains
  189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  272 MET
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0980
   chunk 61 optimal weight:    0.6980
   chunk 131 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 128 optimal weight:    0.4980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** D  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.181266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.119675 restraints weight = 22403.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.65
r_work: 0.3259 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14026  Z= 0.143
  Angle     :  0.542   6.385  19573  Z= 0.305
  Chirality :  0.040   0.172   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.468 175.490   3008
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.75 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.89 (0.23), residues: 1347
  helix:  2.06 (0.20), residues: 641
  sheet: -0.42 (0.37), residues: 198
  loop : -0.90 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 296 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.012   0.001   PHE A  89 
 TYR   0.013   0.001   TYR B 309 
 ARG   0.008   0.000   ARG B 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  655)
  hydrogen bonds       : angle       3.72354 ( 1812)
  covalent geometry    : bond        0.00322 (14026)
  covalent geometry    : angle       0.54195 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 1.464 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7352 (mtp85)
REVERT: B   92 TYR cc_start: 0.8368 (m-80) cc_final: 0.8097 (m-10)
REVERT: B  130 PHE cc_start: 0.6984 (m-80) cc_final: 0.6515 (m-80)
REVERT: C  156 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7150 (ptt90)
REVERT: C  253 GLN cc_start: 0.7952 (tt0) cc_final: 0.7708 (mt0)
REVERT: D   51 MET cc_start: 0.8611 (ptt) cc_final: 0.8188 (ptt)
REVERT: D   78 SER cc_start: 0.8284 (m) cc_final: 0.7951 (t)
REVERT: E  124 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.6779 (ttp-170)
REVERT: E  172 ASN cc_start: 0.8020 (t0) cc_final: 0.7643 (t0)
REVERT: E  246 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: E  247 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7327 (pm20)
REVERT: F   36 ASP cc_start: 0.7844 (m-30) cc_final: 0.7488 (m-30)
REVERT: F  101 SER cc_start: 0.9131 (t) cc_final: 0.8707 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 201
  average time/residue: 0.2793
  time to fit residues: 80.2545
Evaluate side-chains
  194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  310 SER
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 138 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 96 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0060
   chunk 106 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.180045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117657 restraints weight = 19818.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.50
r_work: 0.3250 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.156
  Angle     :  0.545   6.356  19573  Z= 0.307
  Chirality :  0.040   0.173   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.461 175.878   3008
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.29 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.92 (0.23), residues: 1347
  helix:  2.10 (0.20), residues: 640
  sheet: -0.41 (0.37), residues: 197
  loop : -0.89 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.017   0.001   PHE A  89 
 TYR   0.011   0.001   TYR F 126 
 ARG   0.007   0.000   ARG B 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  655)
  hydrogen bonds       : angle       3.71302 ( 1812)
  covalent geometry    : bond        0.00358 (14026)
  covalent geometry    : angle       0.54497 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 1.356 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7325 (mtp85)
REVERT: B   92 TYR cc_start: 0.8373 (m-80) cc_final: 0.8101 (m-10)
REVERT: B  130 PHE cc_start: 0.6956 (m-80) cc_final: 0.6453 (m-80)
REVERT: B  272 MET cc_start: 0.7537 (mtp) cc_final: 0.7286 (mtp)
REVERT: C  156 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7129 (ptt90)
REVERT: C  253 GLN cc_start: 0.7951 (tt0) cc_final: 0.7703 (mt0)
REVERT: D   51 MET cc_start: 0.8598 (ptt) cc_final: 0.8213 (ptt)
REVERT: D   78 SER cc_start: 0.8308 (m) cc_final: 0.7877 (t)
REVERT: E  124 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.6711 (ttp-170)
REVERT: E  140 MET cc_start: 0.7008 (mmm) cc_final: 0.6806 (mmt)
REVERT: E  172 ASN cc_start: 0.7972 (t0) cc_final: 0.7592 (t0)
REVERT: F   36 ASP cc_start: 0.7836 (m-30) cc_final: 0.7452 (m-30)
REVERT: F  101 SER cc_start: 0.9116 (t) cc_final: 0.8669 (p)
REVERT: F  116 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7334 (mmm-85)
  outliers start: 21
  outliers final: 15
  residues processed: 188
  average time/residue: 0.2911
  time to fit residues: 76.3618
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 145 optimal weight:   40.0000
   chunk 26 optimal weight:    3.9990
   chunk 138 optimal weight:   20.0000
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 139 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.176221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.114721 restraints weight = 16081.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.38
r_work: 0.3180 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14026  Z= 0.227
  Angle     :  0.607   7.568  19573  Z= 0.336
  Chirality :  0.042   0.156   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.607 176.131   3008
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.65 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.69 (0.23), residues: 1347
  helix:  1.88 (0.20), residues: 639
  sheet: -0.55 (0.38), residues: 195
  loop : -0.95 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  83 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.014   0.002   PHE A  89 
 TYR   0.015   0.002   TYR F  26 
 ARG   0.008   0.001   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04286 (  655)
  hydrogen bonds       : angle       3.96016 ( 1812)
  covalent geometry    : bond        0.00535 (14026)
  covalent geometry    : angle       0.60655 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 1.657 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7483 (mtp85)
REVERT: B  130 PHE cc_start: 0.7188 (m-80) cc_final: 0.6763 (m-80)
REVERT: C  156 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7268 (ptt90)
REVERT: D   78 SER cc_start: 0.8401 (m) cc_final: 0.8035 (t)
REVERT: E  172 ASN cc_start: 0.8070 (t0) cc_final: 0.7700 (t0)
REVERT: F  101 SER cc_start: 0.9136 (t) cc_final: 0.8702 (p)
REVERT: F  116 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7411 (mmm-85)
  outliers start: 20
  outliers final: 16
  residues processed: 189
  average time/residue: 0.3454
  time to fit residues: 91.5182
Evaluate side-chains
  178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 105 optimal weight:    0.3980
   chunk 57 optimal weight:    0.8980
   chunk 120 optimal weight:   20.0000
   chunk 139 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
D  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.177638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.114402 restraints weight = 24482.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.90
r_work: 0.3164 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.179
  Angle     :  0.573   9.263  19573  Z= 0.319
  Chirality :  0.041   0.155   2195
  Planarity :  0.004   0.049   2042
  Dihedral  : 24.546 176.014   3008
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.10 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.70 (0.23), residues: 1347
  helix:  1.88 (0.20), residues: 639
  sheet: -0.62 (0.36), residues: 200
  loop : -0.90 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  83 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.016   0.001   PHE C 239 
 TYR   0.015   0.001   TYR F 126 
 ARG   0.015   0.000   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  655)
  hydrogen bonds       : angle       3.87217 ( 1812)
  covalent geometry    : bond        0.00415 (14026)
  covalent geometry    : angle       0.57262 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 1.161 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7479 (mtp85)
REVERT: B  130 PHE cc_start: 0.7049 (m-80) cc_final: 0.6559 (m-80)
REVERT: C  156 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7254 (ptt90)
REVERT: D   78 SER cc_start: 0.8352 (m) cc_final: 0.7993 (t)
REVERT: E  172 ASN cc_start: 0.8096 (t0) cc_final: 0.7702 (t0)
REVERT: F  101 SER cc_start: 0.9149 (t) cc_final: 0.8688 (p)
REVERT: F  116 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7371 (mmm-85)
  outliers start: 18
  outliers final: 16
  residues processed: 178
  average time/residue: 0.2878
  time to fit residues: 71.7457
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 121 optimal weight:    3.9990
   chunk 118 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 116 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
F 127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.178859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116334 restraints weight = 18889.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.52
r_work: 0.3219 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.168
  Angle     :  0.566   9.306  19573  Z= 0.316
  Chirality :  0.040   0.167   2195
  Planarity :  0.004   0.067   2042
  Dihedral  : 24.513 175.939   3008
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.73 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.73 (0.23), residues: 1347
  helix:  1.89 (0.20), residues: 640
  sheet: -0.60 (0.36), residues: 200
  loop : -0.86 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.014   0.001   PHE C 239 
 TYR   0.024   0.001   TYR F 126 
 ARG   0.016   0.000   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  655)
  hydrogen bonds       : angle       3.84244 ( 1812)
  covalent geometry    : bond        0.00389 (14026)
  covalent geometry    : angle       0.56647 (19573)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 1.332 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7363 (mtp85)
REVERT: B  130 PHE cc_start: 0.7023 (m-80) cc_final: 0.6540 (m-80)
REVERT: B  257 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7952 (mm)
REVERT: C  156 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7270 (ptt90)
REVERT: D   78 SER cc_start: 0.8329 (m) cc_final: 0.7983 (t)
REVERT: E  124 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.6827 (ttp-170)
REVERT: E  172 ASN cc_start: 0.8155 (t0) cc_final: 0.7778 (t0)
REVERT: F  101 SER cc_start: 0.9121 (t) cc_final: 0.8670 (p)
REVERT: F  116 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7417 (mmm-85)
  outliers start: 17
  outliers final: 15
  residues processed: 178
  average time/residue: 0.2855
  time to fit residues: 71.4157
Evaluate side-chains
  181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0030
   chunk 137 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0370
   chunk 83 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0570
   chunk 81 optimal weight:    0.0270
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.1644

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.183261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.122243 restraints weight = 20905.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.62
r_work: 0.3288 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14026  Z= 0.132
  Angle     :  0.537   8.787  19573  Z= 0.301
  Chirality :  0.039   0.149   2195
  Planarity :  0.004   0.063   2042
  Dihedral  : 24.388 176.178   3008
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.73 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.90 (0.23), residues: 1347
  helix:  2.02 (0.20), residues: 642
  sheet: -0.53 (0.36), residues: 200
  loop : -0.77 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  83 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.014   0.001   PHE A  89 
 TYR   0.015   0.001   TYR F 126 
 ARG   0.015   0.001   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  655)
  hydrogen bonds       : angle       3.69550 ( 1812)
  covalent geometry    : bond        0.00291 (14026)
  covalent geometry    : angle       0.53726 (19573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9735.69 seconds
wall clock time: 167 minutes 52.56 seconds (10072.56 seconds total)