Starting phenix.real_space_refine
on Mon Apr 28 12:01:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qot_18541/04_2025/8qot_18541.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4791      2.51       5
     N    1243      2.21       5
     O    1416      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7493
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2320
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
      Conformer: "B"
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
          bond proxies already assigned to first conformer: 2355
    Chain: "B"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 948
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
    Chain: "H"
      Number of atoms: 1708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1708
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 10
    Chain: "L"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1586
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198}
    Chain: "K"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 931
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 320 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 320 " occ=0.50
  Time building chain proxies: 5.65, per 1000 atoms: 0.75
  Number of scatterers: 7493
  At special positions: 0
  Unit cell: (66.3612, 89.7828, 161.999, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1416      8.00
     N    1243      7.00
     C    4791      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  92 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1802

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 18 sheets defined
      30.2% alpha, 37.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 95
    Processing helix  chain 'A' and resid 101 through 131
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 136 through 170
      removed outlier: 3.676A  pdb=" N   CYS A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 205
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 224 through 258
      removed outlier: 3.735A  pdb=" N   TRP A 228 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
      Proline residue:  A 244  - end of helix
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.863A  pdb=" N   MET A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 306
      removed outlier: 3.786A  pdb=" N   LEU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'A' and resid 311 through 339
      removed outlier: 3.793A  pdb=" N   SER A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   TRP A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   HIS A 319 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   SER A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   CYS A 330 " --> pdb=" O   TYR A 326 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 341 through 350
      removed outlier: 4.250A  pdb=" N   GLU A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.810A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.514A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 98 through 100C
    Processing helix  chain 'H' and resid 156 through 158
      No H-bonds generated for 'chain 'H' and resid 156 through 158'
    Processing helix  chain 'H' and resid 187 through 189
      No H-bonds generated for 'chain 'H' and resid 187 through 189'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.688A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 183 through 189
      removed outlier: 3.676A  pdb=" N   HIS L 189 " --> pdb=" O   ASP L 185 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 83 through 87
      removed outlier: 3.855A  pdb=" N   THR K  87 " --> pdb=" O   PRO K  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210
      removed outlier: 3.532A  pdb=" N   THR A 218 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9
      removed outlier: 3.786A  pdb=" N   SER B   9 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14
      removed outlier: 6.167A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA B  51 " --> pdb=" O   TRP B  38 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ARG B  40 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   LEU B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14
      removed outlier: 6.167A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.679A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.998A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR H  50 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER H  58 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124
      removed outlier: 3.753A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124
      removed outlier: 3.753A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.609A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.553A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13
    Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.627A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.601A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.859A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER K  25 " --> pdb=" O   GLN K   3 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN K   5 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 57 through 59
      removed outlier: 5.636A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE K  94 " --> pdb=" O   TYR K 102 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   TYR K 102 " --> pdb=" O   ILE K  94 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 59
      removed outlier: 5.636A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1141 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2338
        1.35 -     1.47: 2075
        1.47 -     1.59: 3200
        1.59 -     1.71: 0
        1.71 -     1.83: 61
  Bond restraints: 7674
  Sorted by residual:
  bond pdb=" N   VAL K  69 "
       pdb=" CA  VAL K  69 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.14e-02 7.69e+03 6.73e+00
  bond pdb=" CA  SER K  70 "
       pdb=" CB  SER K  70 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 1.69e-02 3.50e+03 5.97e+00
  bond pdb=" N   SER K  70 "
       pdb=" CA  SER K  70 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.20e-02 6.94e+03 5.68e+00
  bond pdb=" N   ARG K  71 "
       pdb=" CA  ARG K  71 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.026 1.22e-02 6.72e+03 4.66e+00
  bond pdb=" N   ASP K  72 "
       pdb=" CA  ASP K  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.27e-02 6.20e+03 4.45e+00
  ... (remaining 7669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 10124
        1.57 -     3.14: 254
        3.14 -     4.70: 45
        4.70 -     6.27: 10
        6.27 -     7.84: 1
  Bond angle restraints: 10434
  Sorted by residual:
  angle pdb=" CA  ARG A 258 "
        pdb=" CB  ARG A 258 "
        pdb=" CG  ARG A 258 "
      ideal   model   delta    sigma   weight residual
     114.10  121.94   -7.84 2.00e+00 2.50e-01 1.54e+01
  angle pdb=" N   THR H 160 "
        pdb=" CA  THR H 160 "
        pdb=" C   THR H 160 "
      ideal   model   delta    sigma   weight residual
     114.56  110.30    4.26 1.27e+00 6.20e-01 1.12e+01
  angle pdb=" C   LEU A 257 "
        pdb=" N   ARG A 258 "
        pdb=" CA  ARG A 258 "
      ideal   model   delta    sigma   weight residual
     122.73  117.58    5.15 1.61e+00 3.86e-01 1.02e+01
  angle pdb=" CA  ARG K  71 "
        pdb=" C   ARG K  71 "
        pdb=" O   ARG K  71 "
      ideal   model   delta    sigma   weight residual
     120.80  117.88    2.92 1.11e+00 8.12e-01 6.94e+00
  angle pdb=" CA  VAL K  69 "
        pdb=" C   VAL K  69 "
        pdb=" O   VAL K  69 "
      ideal   model   delta    sigma   weight residual
     120.67  117.65    3.02 1.17e+00 7.31e-01 6.64e+00
  ... (remaining 10429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4182
       17.98 -    35.95: 279
       35.95 -    53.93: 46
       53.93 -    71.90: 7
       71.90 -    89.88: 8
  Dihedral angle restraints: 4522
    sinusoidal: 1698
      harmonic: 2824
  Sorted by residual:
  dihedral pdb=" CA  ARG A  95 "
           pdb=" C   ARG A  95 "
           pdb=" N   TYR A  96 "
           pdb=" CA  TYR A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.70  -27.30     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  92 "
           pdb=" CB  CYS K  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.46   38.54     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CA  LYS A 100 "
           pdb=" C   LYS A 100 "
           pdb=" N   THR A 101 "
           pdb=" CA  THR A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.13   20.87     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 4519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 781
       0.037 -    0.074: 292
       0.074 -    0.111: 80
       0.111 -    0.148: 23
       0.148 -    0.186: 3
  Chirality restraints: 1179
  Sorted by residual:
  chirality pdb=" CA  ARG A 258 "
            pdb=" N   ARG A 258 "
            pdb=" C   ARG A 258 "
            pdb=" CB  ARG A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" CA  VAL K  69 "
            pdb=" N   VAL K  69 "
            pdb=" C   VAL K  69 "
            pdb=" CB  VAL K  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CB  THR B  35 "
            pdb=" CA  THR B  35 "
            pdb=" OG1 THR B  35 "
            pdb=" CG2 THR B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  ... (remaining 1176 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 238 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   ILE A 238 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A 238 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 239 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 239 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.51e+00
        pdb=" C   PHE A 239 "    0.027 2.00e-02 2.50e+03
        pdb=" O   PHE A 239 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 240 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K  71 "    0.136 9.50e-02 1.11e+02   6.10e-02 2.29e+00
        pdb=" NE  ARG K  71 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG K  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG K  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG K  71 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1004
        2.76 -     3.29: 6956
        3.29 -     3.83: 11499
        3.83 -     4.36: 12874
        4.36 -     4.90: 23368
  Nonbonded interactions: 55701
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 290 "
            pdb=" OG1 THR A 294 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   PRO A 122 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" ND2 ASN H 100H"
            pdb=" O   ALA L  32 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OG  SER L  63 "
            pdb=" OG1 THR L  74 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LYS A 100 "
            pdb=" OG1 THR A 101 "
     model   vdw
     2.304 3.040
  ... (remaining 55696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.260
  Find NCS groups from input model:        0.090
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
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   0.045   7681  Z= 0.195
  Angle     :  0.626   7.838  10448  Z= 0.344
  Chirality :  0.043   0.186   1179
  Planarity :  0.004   0.061   1304
  Dihedral  : 12.782  89.878   2699
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.08 (0.26), residues: 959
  helix:  1.34 (0.31), residues: 247
  sheet:  0.33 (0.30), residues: 292
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.021   0.002   PHE L 118 
 TYR   0.024   0.002   TYR L  55 
 ARG   0.004   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22505 (  383)
  hydrogen bonds       : angle       8.18482 ( 1141)
  SS BOND              : bond        0.00709 (    7)
  SS BOND              : angle       1.45362 (   14)
  covalent geometry    : bond        0.00407 ( 7674)
  covalent geometry    : angle       0.62433 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  158 LEU cc_start: 0.8111 (tp) cc_final: 0.7897 (tt)
REVERT: L   82 ASP cc_start: 0.7321 (m-30) cc_final: 0.7050 (m-30)
REVERT: K  100 TYR cc_start: 0.8840 (m-80) cc_final: 0.8630 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1912
  time to fit residues: 49.3179
Evaluate side-chains
  154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0670
   chunk 28 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  97 GLN
L 124 GLN
L 160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.142737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111035 restraints weight = 32752.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 5.52
r_work: 0.3257 rms_B_bonded: 5.36 restraints_weight: 2.0000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    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 = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7681  Z= 0.143
  Angle     :  0.645  11.943  10448  Z= 0.337
  Chirality :  0.043   0.168   1179
  Planarity :  0.004   0.032   1304
  Dihedral  :  4.542  25.821   1061
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.52 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.50 (0.27), residues: 959
  helix:  1.51 (0.32), residues: 247
  sheet:  0.84 (0.29), residues: 307
  loop : -0.81 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  99 
 HIS   0.004   0.001   HIS H 164 
 PHE   0.018   0.002   PHE A 108 
 TYR   0.019   0.001   TYR K  79 
 ARG   0.011   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  383)
  hydrogen bonds       : angle       5.91019 ( 1141)
  SS BOND              : bond        0.00776 (    7)
  SS BOND              : angle       1.48515 (   14)
  covalent geometry    : bond        0.00307 ( 7674)
  covalent geometry    : angle       0.64326 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 THR cc_start: 0.7242 (m) cc_final: 0.7019 (p)
REVERT: A  158 LEU cc_start: 0.8122 (tp) cc_final: 0.7917 (tt)
REVERT: A  255 MET cc_start: 0.5728 (mmt) cc_final: 0.4793 (mmp)
REVERT: A  336 TYR cc_start: 0.8485 (m-80) cc_final: 0.8232 (m-80)
REVERT: B  102 TYR cc_start: 0.8135 (m-80) cc_final: 0.7884 (m-80)
REVERT: L   82 ASP cc_start: 0.8135 (m-30) cc_final: 0.7658 (m-30)
REVERT: L  161 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: K   34 MET cc_start: 0.8661 (mmm) cc_final: 0.8181 (mmm)
REVERT: K   82 ASN cc_start: 0.8448 (m110) cc_final: 0.8221 (m-40)
REVERT: K  100 TYR cc_start: 0.8901 (m-80) cc_final: 0.8660 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 164
  average time/residue: 0.2080
  time to fit residues: 45.0934
Evaluate side-chains
  155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  184 VAL
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107865 restraints weight = 30022.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 5.22
r_work: 0.3226 rms_B_bonded: 5.13 restraints_weight: 2.0000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7681  Z= 0.168
  Angle     :  0.622   9.455  10448  Z= 0.326
  Chirality :  0.043   0.222   1179
  Planarity :  0.004   0.045   1304
  Dihedral  :  4.494  27.021   1061
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.18 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.68 (0.27), residues: 959
  helix:  1.51 (0.33), residues: 247
  sheet:  1.18 (0.29), residues: 302
  loop : -0.77 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  99 
 HIS   0.005   0.001   HIS H 164 
 PHE   0.020   0.002   PHE A 108 
 TYR   0.016   0.001   TYR K  79 
 ARG   0.005   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  383)
  hydrogen bonds       : angle       5.55274 ( 1141)
  SS BOND              : bond        0.00784 (    7)
  SS BOND              : angle       1.51838 (   14)
  covalent geometry    : bond        0.00379 ( 7674)
  covalent geometry    : angle       0.62020 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 TRP cc_start: 0.8443 (t-100) cc_final: 0.8107 (t-100)
REVERT: A  153 THR cc_start: 0.7285 (m) cc_final: 0.7044 (p)
REVERT: A  336 TYR cc_start: 0.8544 (m-80) cc_final: 0.8307 (m-80)
REVERT: B  102 TYR cc_start: 0.8204 (m-80) cc_final: 0.7951 (m-80)
REVERT: H  116 THR cc_start: 0.8308 (m) cc_final: 0.7858 (t)
REVERT: H  171 GLN cc_start: 0.8633 (mt0) cc_final: 0.8051 (mt0)
REVERT: H  177 SER cc_start: 0.8902 (p) cc_final: 0.8447 (m)
REVERT: L   81 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: L   82 ASP cc_start: 0.8128 (m-30) cc_final: 0.7532 (m-30)
REVERT: K   34 MET cc_start: 0.8634 (mmm) cc_final: 0.8168 (mmm)
REVERT: K  100 TYR cc_start: 0.9005 (m-80) cc_final: 0.8753 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 163
  average time/residue: 0.1942
  time to fit residues: 42.6785
Evaluate side-chains
  157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN
K  82AASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.106509 restraints weight = 36054.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 5.86
r_work: 0.3185 rms_B_bonded: 5.65 restraints_weight: 2.0000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7681  Z= 0.161
  Angle     :  0.603   9.549  10448  Z= 0.316
  Chirality :  0.042   0.168   1179
  Planarity :  0.004   0.043   1304
  Dihedral  :  4.471  27.472   1061
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.99 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.76 (0.27), residues: 959
  helix:  1.59 (0.33), residues: 247
  sheet:  1.20 (0.28), residues: 320
  loop : -0.81 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  99 
 HIS   0.005   0.001   HIS H 164 
 PHE   0.021   0.002   PHE A 338 
 TYR   0.016   0.001   TYR K  79 
 ARG   0.007   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  383)
  hydrogen bonds       : angle       5.31472 ( 1141)
  SS BOND              : bond        0.00623 (    7)
  SS BOND              : angle       1.43985 (   14)
  covalent geometry    : bond        0.00364 ( 7674)
  covalent geometry    : angle       0.60115 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  133 TRP cc_start: 0.8439 (t-100) cc_final: 0.8089 (t-100)
REVERT: A  251 CYS cc_start: 0.7519 (m) cc_final: 0.7034 (m)
REVERT: A  255 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.4906 (mmp)
REVERT: A  336 TYR cc_start: 0.8570 (m-80) cc_final: 0.8273 (m-80)
REVERT: B  102 TYR cc_start: 0.8270 (m-80) cc_final: 0.8024 (m-80)
REVERT: H   83 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7575 (mtm-85)
REVERT: H  116 THR cc_start: 0.8415 (m) cc_final: 0.7994 (t)
REVERT: H  171 GLN cc_start: 0.8710 (mt0) cc_final: 0.8070 (mt0)
REVERT: H  177 SER cc_start: 0.8943 (p) cc_final: 0.8440 (m)
REVERT: L   81 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7648 (tm-30)
REVERT: L   82 ASP cc_start: 0.8231 (m-30) cc_final: 0.7652 (m-30)
REVERT: L  161 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8320 (mt-10)
REVERT: K   34 MET cc_start: 0.8669 (mmm) cc_final: 0.8264 (mmm)
REVERT: K   70 SER cc_start: 0.8665 (t) cc_final: 0.7962 (p)
REVERT: K  100 TYR cc_start: 0.9027 (m-80) cc_final: 0.8629 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 162
  average time/residue: 0.1858
  time to fit residues: 40.9526
Evaluate side-chains
  167 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.0020
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 88 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 197 ASN
K  82AASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.138274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.107311 restraints weight = 28433.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 5.12
r_work: 0.3218 rms_B_bonded: 5.07 restraints_weight: 2.0000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7681  Z= 0.147
  Angle     :  0.599  10.501  10448  Z= 0.313
  Chirality :  0.042   0.172   1179
  Planarity :  0.004   0.042   1304
  Dihedral  :  4.419  28.161   1061
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.99 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.77 (0.27), residues: 959
  helix:  1.63 (0.33), residues: 247
  sheet:  1.24 (0.28), residues: 324
  loop : -0.89 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  99 
 HIS   0.004   0.001   HIS H 164 
 PHE   0.019   0.001   PHE A 108 
 TYR   0.015   0.001   TYR K  79 
 ARG   0.008   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  383)
  hydrogen bonds       : angle       5.17741 ( 1141)
  SS BOND              : bond        0.00578 (    7)
  SS BOND              : angle       1.40450 (   14)
  covalent geometry    : bond        0.00329 ( 7674)
  covalent geometry    : angle       0.59722 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  133 TRP cc_start: 0.8494 (t-100) cc_final: 0.8070 (t-100)
REVERT: A  336 TYR cc_start: 0.8522 (m-80) cc_final: 0.8174 (m-80)
REVERT: B  102 TYR cc_start: 0.8185 (m-80) cc_final: 0.7967 (m-80)
REVERT: H   83 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7514 (mtm-85)
REVERT: H  116 THR cc_start: 0.8387 (m) cc_final: 0.7992 (t)
REVERT: H  171 GLN cc_start: 0.8668 (mt0) cc_final: 0.8021 (mt0)
REVERT: H  177 SER cc_start: 0.8910 (p) cc_final: 0.8424 (m)
REVERT: L   81 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7673 (tm-30)
REVERT: L   82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7616 (m-30)
REVERT: K   34 MET cc_start: 0.8574 (mmm) cc_final: 0.8283 (mpp)
REVERT: K  100 TYR cc_start: 0.9023 (m-80) cc_final: 0.8706 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 163
  average time/residue: 0.1800
  time to fit residues: 40.3706
Evaluate side-chains
  166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  179 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0060
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0060
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.2770

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  82AASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.139847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.109324 restraints weight = 27455.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 4.95
r_work: 0.3255 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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      :  0.002   0.026   7681  Z= 0.114
  Angle     :  0.588  10.649  10448  Z= 0.302
  Chirality :  0.042   0.204   1179
  Planarity :  0.004   0.042   1304
  Dihedral  :  4.243  27.973   1061
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.72 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.85 (0.27), residues: 959
  helix:  1.67 (0.33), residues: 248
  sheet:  1.30 (0.28), residues: 326
  loop : -0.85 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 192 
 HIS   0.001   0.000   HIS H 200 
 PHE   0.023   0.001   PHE A 338 
 TYR   0.013   0.001   TYR A 252 
 ARG   0.009   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  383)
  hydrogen bonds       : angle       4.98012 ( 1141)
  SS BOND              : bond        0.00482 (    7)
  SS BOND              : angle       1.20008 (   14)
  covalent geometry    : bond        0.00241 ( 7674)
  covalent geometry    : angle       0.58694 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 TRP cc_start: 0.8456 (t-100) cc_final: 0.8007 (t-100)
REVERT: A  336 TYR cc_start: 0.8475 (m-80) cc_final: 0.8191 (m-80)
REVERT: H   83 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7549 (mtm-85)
REVERT: H  116 THR cc_start: 0.8347 (m) cc_final: 0.7952 (t)
REVERT: L   42 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8480 (mmmm)
REVERT: L   79 GLN cc_start: 0.8603 (mm110) cc_final: 0.8221 (mm-40)
REVERT: L   81 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7666 (tm-30)
REVERT: L   82 ASP cc_start: 0.8180 (m-30) cc_final: 0.7659 (m-30)
REVERT: K   34 MET cc_start: 0.8515 (mmm) cc_final: 0.8232 (mpp)
REVERT: K   82 MET cc_start: 0.7479 (mtp) cc_final: 0.7080 (ttm)
REVERT: K  100 TYR cc_start: 0.8931 (m-80) cc_final: 0.8701 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 157
  average time/residue: 0.2032
  time to fit residues: 42.9121
Evaluate side-chains
  153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0570
   chunk 74 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
H  35 HIS
H 171 GLN
L  89 GLN
K  82AASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.107002 restraints weight = 31037.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 5.38
r_work: 0.3205 rms_B_bonded: 5.28 restraints_weight: 2.0000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7681  Z= 0.147
  Angle     :  0.602  10.531  10448  Z= 0.310
  Chirality :  0.042   0.192   1179
  Planarity :  0.004   0.041   1304
  Dihedral  :  4.310  27.430   1061
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.81 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.27), residues: 959
  helix:  1.64 (0.33), residues: 249
  sheet:  1.43 (0.29), residues: 322
  loop : -0.87 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.019   0.001   PHE A 108 
 TYR   0.018   0.001   TYR A 299 
 ARG   0.010   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  383)
  hydrogen bonds       : angle       5.01993 ( 1141)
  SS BOND              : bond        0.00578 (    7)
  SS BOND              : angle       1.29797 (   14)
  covalent geometry    : bond        0.00331 ( 7674)
  covalent geometry    : angle       0.60072 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  336 TYR cc_start: 0.8510 (m-80) cc_final: 0.8178 (m-80)
REVERT: B  102 TYR cc_start: 0.8247 (m-80) cc_final: 0.8035 (m-80)
REVERT: H   83 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7560 (mtm-85)
REVERT: H  116 THR cc_start: 0.8417 (m) cc_final: 0.8029 (t)
REVERT: H  171 GLN cc_start: 0.8699 (mt0) cc_final: 0.8105 (mt0)
REVERT: H  177 SER cc_start: 0.8960 (p) cc_final: 0.8477 (m)
REVERT: L   42 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8497 (mmmm)
REVERT: L   79 GLN cc_start: 0.8629 (mm110) cc_final: 0.8232 (mm-40)
REVERT: L   81 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7694 (tm-30)
REVERT: L   82 ASP cc_start: 0.8181 (m-30) cc_final: 0.7680 (m-30)
REVERT: K   34 MET cc_start: 0.8554 (mmm) cc_final: 0.8261 (mpp)
REVERT: K   82 MET cc_start: 0.7544 (mtp) cc_final: 0.7139 (ttm)
REVERT: K  100 TYR cc_start: 0.8923 (m-80) cc_final: 0.8679 (m-80)
  outliers start: 19
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1804
  time to fit residues: 36.6524
Evaluate side-chains
  156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0570
   chunk 56 optimal weight:    0.2980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
K  82AASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.138396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.107448 restraints weight = 31167.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 5.33
r_work: 0.3212 rms_B_bonded: 5.24 restraints_weight: 2.0000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7681  Z= 0.135
  Angle     :  0.605  10.854  10448  Z= 0.310
  Chirality :  0.042   0.191   1179
  Planarity :  0.003   0.039   1304
  Dihedral  :  4.300  28.001   1061
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.53 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.27), residues: 959
  helix:  1.68 (0.33), residues: 249
  sheet:  1.49 (0.29), residues: 319
  loop : -0.89 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.018   0.001   PHE A 338 
 TYR   0.020   0.001   TYR A 299 
 ARG   0.008   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  383)
  hydrogen bonds       : angle       4.97098 ( 1141)
  SS BOND              : bond        0.00555 (    7)
  SS BOND              : angle       1.33474 (   14)
  covalent geometry    : bond        0.00298 ( 7674)
  covalent geometry    : angle       0.60363 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  336 TYR cc_start: 0.8506 (m-80) cc_final: 0.8190 (m-80)
REVERT: B  102 TYR cc_start: 0.8223 (m-80) cc_final: 0.7988 (m-80)
REVERT: H   83 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7561 (mtm-85)
REVERT: H  116 THR cc_start: 0.8412 (m) cc_final: 0.8036 (t)
REVERT: H  171 GLN cc_start: 0.8691 (mt0) cc_final: 0.8041 (mt0)
REVERT: H  177 SER cc_start: 0.8932 (p) cc_final: 0.8434 (m)
REVERT: L   42 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8492 (mmmm)
REVERT: L   79 GLN cc_start: 0.8624 (mm110) cc_final: 0.8235 (mm-40)
REVERT: L   81 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: L   82 ASP cc_start: 0.8164 (m-30) cc_final: 0.7679 (m-30)
REVERT: L  187 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7790 (mt-10)
REVERT: K   34 MET cc_start: 0.8557 (mmm) cc_final: 0.8266 (mpp)
REVERT: K   82 MET cc_start: 0.7511 (mtp) cc_final: 0.7123 (ttm)
REVERT: K  100 TYR cc_start: 0.8923 (m-80) cc_final: 0.8705 (m-80)
  outliers start: 22
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1829
  time to fit residues: 37.7630
Evaluate side-chains
  152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 93 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
K  82AASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.137934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109779 restraints weight = 17780.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 3.91
r_work: 0.3283 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7681  Z= 0.145
  Angle     :  0.618  10.924  10448  Z= 0.315
  Chirality :  0.042   0.188   1179
  Planarity :  0.004   0.039   1304
  Dihedral  :  4.323  28.642   1061
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.53 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.27), residues: 959
  helix:  1.64 (0.33), residues: 249
  sheet:  1.50 (0.29), residues: 320
  loop : -0.92 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.020   0.001   PHE A 350 
 TYR   0.021   0.001   TYR A 299 
 ARG   0.009   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  383)
  hydrogen bonds       : angle       4.99730 ( 1141)
  SS BOND              : bond        0.00567 (    7)
  SS BOND              : angle       1.32582 (   14)
  covalent geometry    : bond        0.00327 ( 7674)
  covalent geometry    : angle       0.61692 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 TYR cc_start: 0.8427 (m-80) cc_final: 0.8097 (m-80)
REVERT: H   83 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7440 (mtm-85)
REVERT: H  116 THR cc_start: 0.8374 (m) cc_final: 0.7997 (t)
REVERT: L   42 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8453 (mmmm)
REVERT: L   79 GLN cc_start: 0.8578 (mm110) cc_final: 0.8171 (mm-40)
REVERT: L   81 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: L   82 ASP cc_start: 0.8076 (m-30) cc_final: 0.7572 (m-30)
REVERT: L  187 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7695 (mt-10)
REVERT: K   34 MET cc_start: 0.8461 (mmm) cc_final: 0.8158 (mpp)
REVERT: K   82 MET cc_start: 0.7371 (mtp) cc_final: 0.7009 (ttm)
REVERT: K  100 TYR cc_start: 0.8887 (m-80) cc_final: 0.8643 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1904
  time to fit residues: 39.4669
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 0 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
H 171 GLN
L  90 GLN
K  82AASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.107821 restraints weight = 29679.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 5.18
r_work: 0.3223 rms_B_bonded: 5.12 restraints_weight: 2.0000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3222
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3222
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7681  Z= 0.129
  Angle     :  0.610  11.208  10448  Z= 0.313
  Chirality :  0.042   0.184   1179
  Planarity :  0.004   0.041   1304
  Dihedral  :  4.293  28.727   1061
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.65 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.98 (0.27), residues: 959
  helix:  1.73 (0.33), residues: 249
  sheet:  1.55 (0.29), residues: 319
  loop : -0.87 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.026   0.001   PHE A 338 
 TYR   0.020   0.001   TYR A 299 
 ARG   0.009   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  383)
  hydrogen bonds       : angle       4.90664 ( 1141)
  SS BOND              : bond        0.00524 (    7)
  SS BOND              : angle       1.26939 (   14)
  covalent geometry    : bond        0.00283 ( 7674)
  covalent geometry    : angle       0.60889 (10434)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  336 TYR cc_start: 0.8486 (m-80) cc_final: 0.8186 (m-80)
REVERT: B  102 TYR cc_start: 0.8241 (m-80) cc_final: 0.7992 (m-80)
REVERT: H   83 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7510 (mtm-85)
REVERT: H  116 THR cc_start: 0.8394 (m) cc_final: 0.8020 (t)
REVERT: H  171 GLN cc_start: 0.8659 (mt0) cc_final: 0.8155 (mt0)
REVERT: H  177 SER cc_start: 0.9003 (p) cc_final: 0.8606 (m)
REVERT: L   42 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8490 (mmmm)
REVERT: L   79 GLN cc_start: 0.8625 (mm110) cc_final: 0.8216 (mm-40)
REVERT: L   81 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: L   82 ASP cc_start: 0.8155 (m-30) cc_final: 0.7669 (m-30)
REVERT: L  187 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7792 (mt-10)
REVERT: K   34 MET cc_start: 0.8568 (mmm) cc_final: 0.8269 (mpp)
REVERT: K   82 MET cc_start: 0.7551 (mtp) cc_final: 0.7155 (ttm)
REVERT: K  100 TYR cc_start: 0.8881 (m-80) cc_final: 0.8641 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1902
  time to fit residues: 39.2284
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 47 optimal weight:    0.1980
   chunk 19 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0070
   chunk 49 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
K  82AASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.138880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.107553 restraints weight = 32205.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 5.46
r_work: 0.3215 rms_B_bonded: 5.33 restraints_weight: 2.0000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7681  Z= 0.123
  Angle     :  0.622  11.162  10448  Z= 0.320
  Chirality :  0.042   0.208   1179
  Planarity :  0.004   0.046   1304
  Dihedral  :  4.308  28.768   1061
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.26 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  1.00 (0.27), residues: 959
  helix:  1.70 (0.33), residues: 249
  sheet:  1.57 (0.29), residues: 319
  loop : -0.83 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  99 
 HIS   0.002   0.001   HIS H 164 
 PHE   0.026   0.001   PHE A 338 
 TYR   0.020   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03830 (  383)
  hydrogen bonds       : angle       4.90467 ( 1141)
  SS BOND              : bond        0.00507 (    7)
  SS BOND              : angle       1.22836 (   14)
  covalent geometry    : bond        0.00266 ( 7674)
  covalent geometry    : angle       0.62036 (10434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4411.38 seconds
wall clock time: 76 minutes 15.67 seconds (4575.67 seconds total)