Starting phenix.real_space_refine
on Wed Sep 17 12:29:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vuv_43541/09_2025/8vuv_43541.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 149 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5449      2.51       5
     N    1465      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8586
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2835
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 18, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "H"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1496
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "L"
      Number of atoms: 1583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1583
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2672
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 14, 'TRANS': 342}
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 13, 'HIS:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 109
  Time building chain proxies: 2.14, per 1000 atoms: 0.25
  Number of scatterers: 8586
  At special positions: 0
  Unit cell: (102.72, 101.864, 145.52, 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      36     16.00
     O    1636      8.00
     N    1465      7.00
     C    5449      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 137 " - pdb=" SG  CYS H 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  86 " - pdb=" SG  CYS B 321 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 499.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2154

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 19 sheets defined
      25.2% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 54
      removed outlier: 3.573A  pdb=" N   GLU A  39 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   HIS A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY A  54 " --> pdb=" O   ASN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 86
    Processing helix  chain 'A' and resid 104 through 114
      removed outlier: 3.901A  pdb=" N   SER A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 159
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 3.809A  pdb=" N   ALA A 175 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A 176 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 213
    Processing helix  chain 'A' and resid 224 through 238
    Processing helix  chain 'A' and resid 276 through 296
      removed outlier: 3.571A  pdb=" N   HIS A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 326
      removed outlier: 3.804A  pdb=" N   PHE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 184 through 186
      No H-bonds generated for 'chain 'H' and resid 184 through 186'
    Processing helix  chain 'L' and resid 125 through 129
    Processing helix  chain 'L' and resid 185 through 190
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.874A  pdb=" N   ALA B  53 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   GLU B  55 " --> pdb=" O   LYS B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 92
      removed outlier: 3.656A  pdb=" N   ARG B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 119
      removed outlier: 3.994A  pdb=" N   ILE B 111 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 132
      removed outlier: 3.887A  pdb=" N   SER B 130 " --> pdb=" O   HIS B 127 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   MET B 132 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 164
      removed outlier: 3.644A  pdb=" N   GLN B 153 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TYR B 164 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 190
    Processing helix  chain 'B' and resid 212 through 223
    Processing helix  chain 'B' and resid 233 through 248
      removed outlier: 4.649A  pdb=" N   TYR B 239 " --> pdb=" O   GLU B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.983A  pdb=" N   ALA B 263 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 259 through 264'
    Processing helix  chain 'B' and resid 288 through 312
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.948A  pdb=" N   ILE B 329 " --> pdb=" O   GLU B 326 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   TYR B 330 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 326 through 330'
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.835A  pdb=" N   ASN B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64
      removed outlier: 7.188A  pdb=" N   GLY A  30 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ILE A  90 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194
      removed outlier: 6.624A  pdb=" N   ILE A 164 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   SER A 222 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU A 166 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271
      removed outlier: 6.908A  pdb=" N   TYR A 351 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE A 366 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE A 353 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN A 357 " --> pdb=" O   LYS A 360 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.769A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL H   5 " --> pdb=" O   LYS H  23 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.574A  pdb=" N   THR H 109 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   MET H  93 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN H  39 " --> pdb=" O   MET H  93 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ILE H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   ILE H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ILE H  50 " --> pdb=" O   ARG H  59 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP H  57 " --> pdb=" O   TYR H  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 122 through 126
      removed outlier: 3.866A  pdb=" N   PHE H 124 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU H 138 " --> pdb=" O   PHE H 124 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY H 136 " --> pdb=" O   LEU H 126 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ASP H 141 " --> pdb=" O   TYR H 173 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   TYR H 173 " --> pdb=" O   ASP H 141 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 122 through 126
      removed outlier: 3.866A  pdb=" N   PHE H 124 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU H 138 " --> pdb=" O   PHE H 124 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY H 136 " --> pdb=" O   LEU H 126 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ASP H 141 " --> pdb=" O   TYR H 173 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   TYR H 173 " --> pdb=" O   ASP H 141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 148 through 151
      removed outlier: 4.293A  pdb=" N   TYR H 191 " --> pdb=" O   VAL H 208 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.960A  pdb=" N   THR L   5 " --> pdb=" O   ARG L  24 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LEU L  21 " --> pdb=" O   LEU L  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.462A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 46
    Processing sheet with id=AB3, first strand: chain 'L' and resid 48 through 49
    Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.949A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 131 through 132
    Processing sheet with id=AB6, first strand: chain 'L' and resid 147 through 152
    Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 72
      removed outlier: 6.567A  pdb=" N   ALA B  38 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE B 123 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 199 through 202
      removed outlier: 6.799A  pdb=" N   PHE B 169 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   GLU B 201 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE B 171 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   SER B 170 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 257 through 258
      removed outlier: 4.002A  pdb=" N   VAL B 280 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B 279 " --> pdb=" O   ILE B 365 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY B 377 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LEU B 366 " --> pdb=" O   ARG B 375 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ARG B 375 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 343 through 344

    304 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2802
        1.34 -     1.46: 2078
        1.46 -     1.58: 3844
        1.58 -     1.70: 1
        1.70 -     1.82: 59
  Bond restraints: 8784
  Sorted by residual:
  bond pdb=" CB  PRO B 148 "
       pdb=" CG  PRO B 148 "
    ideal  model  delta    sigma   weight residual
    1.492  1.605 -0.113 5.00e-02 4.00e+02 5.15e+00
  bond pdb=" CB  PRO L  40 "
       pdb=" CG  PRO L  40 "
    ideal  model  delta    sigma   weight residual
    1.492  1.565 -0.073 5.00e-02 4.00e+02 2.13e+00
  bond pdb=" CB  PRO A  98 "
       pdb=" CG  PRO A  98 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.71e+00
  bond pdb=" CB  LYS H 140 "
       pdb=" CG  LYS H 140 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.70e+00
  bond pdb=" CB  MET A 155 "
       pdb=" CG  MET A 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.87e-01
  ... (remaining 8779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 11827
        2.22 -     4.43: 138
        4.43 -     6.65: 16
        6.65 -     8.86: 7
        8.86 -    11.08: 3
  Bond angle restraints: 11991
  Sorted by residual:
  angle pdb=" CA  PRO B 148 "
        pdb=" N   PRO B 148 "
        pdb=" CD  PRO B 148 "
      ideal   model   delta    sigma   weight residual
     112.00  104.92    7.08 1.40e+00 5.10e-01 2.56e+01
  angle pdb=" CA  GLU A 213 "
        pdb=" CB  GLU A 213 "
        pdb=" CG  GLU A 213 "
      ideal   model   delta    sigma   weight residual
     114.10  122.61   -8.51 2.00e+00 2.50e-01 1.81e+01
  angle pdb=" CB  LYS H 140 "
        pdb=" CG  LYS H 140 "
        pdb=" CD  LYS H 140 "
      ideal   model   delta    sigma   weight residual
     111.30  120.34   -9.04 2.30e+00 1.89e-01 1.54e+01
  angle pdb=" CA  LYS H 140 "
        pdb=" CB  LYS H 140 "
        pdb=" CG  LYS H 140 "
      ideal   model   delta    sigma   weight residual
     114.10  121.35   -7.25 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" N   PRO B 148 "
        pdb=" CD  PRO B 148 "
        pdb=" CG  PRO B 148 "
      ideal   model   delta    sigma   weight residual
     103.20   97.93    5.27 1.50e+00 4.44e-01 1.23e+01
  ... (remaining 11986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4455
       17.81 -    35.62: 575
       35.62 -    53.42: 142
       53.42 -    71.23: 23
       71.23 -    89.04: 13
  Dihedral angle restraints: 5208
    sinusoidal: 1860
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" CA  VAL H 101 "
           pdb=" C   VAL H 101 "
           pdb=" N   PHE H 102 "
           pdb=" CA  PHE H 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.87  -36.13     0      5.00e+00 4.00e-02 5.22e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.87  -49.87     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" CA  ASP A 345 "
           pdb=" C   ASP A 345 "
           pdb=" N   ARG A 346 "
           pdb=" CA  ARG A 346 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.52   28.48     0      5.00e+00 4.00e-02 3.24e+01
  ... (remaining 5205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 995
       0.042 -    0.083: 268
       0.083 -    0.124: 107
       0.124 -    0.166: 10
       0.166 -    0.207: 1
  Chirality restraints: 1381
  Sorted by residual:
  chirality pdb=" CA  PRO A  98 "
            pdb=" N   PRO A  98 "
            pdb=" C   PRO A  98 "
            pdb=" CB  PRO A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE A 164 "
            pdb=" N   ILE A 164 "
            pdb=" C   ILE A 164 "
            pdb=" CB  ILE A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 1378 not shown)

  Planarity restraints: 1539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  97 "    0.053 5.00e-02 4.00e+02   8.12e-02 1.05e+01
        pdb=" N   PRO A  98 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A  98 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A  98 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L  39 "    0.046 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO L  40 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO L  40 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO L  40 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 176 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO B 177 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 177 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 177 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1536 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 302
        2.71 -     3.26: 8155
        3.26 -     3.80: 12886
        3.80 -     4.35: 15119
        4.35 -     4.90: 26761
  Nonbonded interactions: 63223
  Sorted by model distance:
  nonbonded pdb=" O   VAL L   3 "
            pdb=" OG  SER L  26 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OE2 GLU B  69 "
            pdb=" NH1 ARG B  92 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" NZ  LYS B 137 "
            pdb=" O   GLU B 354 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" NE2 GLN B  95 "
            pdb=" OE1 GLU B 316 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OD1 ASP A 130 "
            pdb=" OG  SER A 132 "
     model   vdw
     2.260 3.040
  ... (remaining 63218 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             6.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.970
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
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      :  0.003   0.113   8790  Z= 0.128
  Angle     :  0.628  11.075  12003  Z= 0.322
  Chirality :  0.044   0.207   1381
  Planarity :  0.005   0.081   1539
  Dihedral  : 17.327  89.039   3036
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.69 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 33.94 %
    Favored  : 65.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.25), residues: 1144
  helix:  0.80 (0.32), residues: 256
  sheet: -0.49 (0.29), residues: 368
  loop : -1.91 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 187 
 TYR   0.009   0.001   TYR H  94 
 PHE   0.020   0.001   PHE L 100 
 TRP   0.011   0.001   TRP L  98 
 HIS   0.002   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8784)
  covalent geometry    : angle       0.62786 (11991)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       0.88252 (   12)
  hydrogen bonds       : bond        0.21075 (  293)
  hydrogen bonds       : angle       7.63179 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: L   92 ASN cc_start: 0.6900 (t0) cc_final: 0.6680 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1112
  time to fit residues: 15.4650
Evaluate side-chains
  94 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.227338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.202504 restraints weight = 12228.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.192211 restraints weight = 26540.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.185795 restraints weight = 18536.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.186788 restraints weight = 20263.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.186538 restraints weight = 12210.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8790  Z= 0.167
  Angle     :  0.639   8.587  12003  Z= 0.333
  Chirality :  0.046   0.207   1381
  Planarity :  0.005   0.081   1539
  Dihedral  :  4.796  34.224   1237
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.74 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 28.62 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.24), residues: 1144
  helix:  0.63 (0.31), residues: 264
  sheet: -0.53 (0.28), residues: 366
  loop : -1.97 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 187 
 TYR   0.017   0.001   TYR L  49 
 PHE   0.015   0.001   PHE H 102 
 TRP   0.014   0.001   TRP H  33 
 HIS   0.003   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8784)
  covalent geometry    : angle       0.63812 (11991)
  SS BOND              : bond        0.00463 (    6)
  SS BOND              : angle       0.95837 (   12)
  hydrogen bonds       : bond        0.05118 (  293)
  hydrogen bonds       : angle       5.62852 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 95
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7960 (m170)
REVERT: A  166 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8421 (tt)
REVERT: H  140 LYS cc_start: 0.5004 (tppt) cc_final: 0.4677 (tppt)
REVERT: L   92 ASN cc_start: 0.7506 (t0) cc_final: 0.7300 (t0)
  outliers start: 52
  outliers final: 29
  residues processed: 139
  average time/residue: 0.0943
  time to fit residues: 18.3498
Evaluate side-chains
  121 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 90
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  162 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  359 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.225747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.195979 restraints weight = 12287.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.194912 restraints weight = 29243.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.190019 restraints weight = 13000.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.189836 restraints weight = 17904.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.189948 restraints weight = 11776.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8790  Z= 0.133
  Angle     :  0.593   7.590  12003  Z= 0.308
  Chirality :  0.044   0.204   1381
  Planarity :  0.005   0.080   1539
  Dihedral  :  4.598  32.416   1235
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.26 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 28.17 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.25), residues: 1144
  helix:  0.68 (0.31), residues: 266
  sheet: -0.52 (0.28), residues: 366
  loop : -1.92 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 187 
 TYR   0.012   0.001   TYR H  27 
 PHE   0.020   0.001   PHE L 100 
 TRP   0.011   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8784)
  covalent geometry    : angle       0.59297 (11991)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       0.82690 (   12)
  hydrogen bonds       : bond        0.04359 (  293)
  hydrogen bonds       : angle       5.09626 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 92
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8067 (pp)
REVERT: A  162 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7961 (m90)
REVERT: A  166 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8359 (tt)
REVERT: A  213 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6360 (pm20)
REVERT: A  346 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8460 (tpt-90)
REVERT: L   92 ASN cc_start: 0.7397 (t0) cc_final: 0.7174 (t0)
REVERT: B  358 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6976 (tpp)
  outliers start: 51
  outliers final: 31
  residues processed: 134
  average time/residue: 0.1026
  time to fit residues: 19.0325
Evaluate side-chains
  125 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 88
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  162 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   overall best weight:    2.7184

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

Flipped N/Q/H residues before XYZ refinement:
H 196 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.202451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.182056 restraints weight = 11929.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.177574 restraints weight = 21106.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.174728 restraints weight = 21576.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.172791 restraints weight = 25342.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.169727 restraints weight = 23172.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074   8790  Z= 0.326
  Angle     :  0.766   7.904  12003  Z= 0.405
  Chirality :  0.051   0.211   1381
  Planarity :  0.005   0.080   1539
  Dihedral  :  5.419  44.254   1235
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.40 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  9.05 %
    Allowed  : 25.68 %
    Favored  : 65.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.24), residues: 1144
  helix:  0.16 (0.30), residues: 262
  sheet: -0.70 (0.28), residues: 370
  loop : -2.18 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 187 
 TYR   0.019   0.002   TYR L  49 
 PHE   0.018   0.002   PHE B 176 
 TRP   0.023   0.002   TRP H  33 
 HIS   0.008   0.002   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00785 ( 8784)
  covalent geometry    : angle       0.76471 (11991)
  SS BOND              : bond        0.00450 (    6)
  SS BOND              : angle       1.45642 (   12)
  hydrogen bonds       : bond        0.06160 (  293)
  hydrogen bonds       : angle       5.33869 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 92
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (pp)
REVERT: A  166 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: A  209 MET cc_start: 0.7253 (tpp) cc_final: 0.7029 (tpp)
REVERT: A  213 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6805 (pm20)
REVERT: A  346 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8593 (tpt-90)
REVERT: H   98 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7789 (tmm-80)
REVERT: L   92 ASN cc_start: 0.7329 (t0) cc_final: 0.7112 (t0)
REVERT: B  168 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5970 (pt)
REVERT: B  179 TYR cc_start: 0.7956 (p90) cc_final: 0.7729 (p90)
REVERT: B  235 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.3385 (tp30)
  outliers start: 80
  outliers final: 51
  residues processed: 164
  average time/residue: 0.0971
  time to fit residues: 22.1189
Evaluate side-chains
  145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 87
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LYS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  116 SER
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 52 optimal weight:   40.0000
   chunk 100 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0370
   chunk 106 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.207579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.183414 restraints weight = 11810.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.178587 restraints weight = 23723.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.176131 restraints weight = 23927.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173931 restraints weight = 26645.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.171933 restraints weight = 24040.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8790  Z= 0.153
  Angle     :  0.621   7.129  12003  Z= 0.325
  Chirality :  0.045   0.207   1381
  Planarity :  0.005   0.079   1539
  Dihedral  :  4.989  40.802   1235
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.13 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 27.49 %
    Favored  : 65.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.24), residues: 1144
  helix:  0.50 (0.31), residues: 262
  sheet: -0.64 (0.28), residues: 366
  loop : -2.11 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 187 
 TYR   0.011   0.001   TYR L  49 
 PHE   0.020   0.001   PHE B 176 
 TRP   0.014   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8784)
  covalent geometry    : angle       0.62056 (11991)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       0.94412 (   12)
  hydrogen bonds       : bond        0.04487 (  293)
  hydrogen bonds       : angle       4.94917 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 93
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8293 (pp)
REVERT: A  166 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8367 (tt)
REVERT: A  209 MET cc_start: 0.7092 (tpp) cc_final: 0.6822 (tpp)
REVERT: A  213 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6452 (pm20)
REVERT: A  346 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8249 (tpt-90)
REVERT: H   98 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7295 (tmm-80)
REVERT: H  140 LYS cc_start: 0.4738 (tppt) cc_final: 0.4337 (tppt)
REVERT: L   92 ASN cc_start: 0.7275 (t0) cc_final: 0.7056 (t0)
REVERT: B  358 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7022 (tpp)
  outliers start: 61
  outliers final: 43
  residues processed: 144
  average time/residue: 0.1005
  time to fit residues: 19.5311
Evaluate side-chains
  139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 90
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  100 PHE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 77 optimal weight:   40.0000
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.207613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.187389 restraints weight = 11634.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.183809 restraints weight = 21538.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.180520 restraints weight = 19911.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.169309 restraints weight = 19477.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163469 restraints weight = 27863.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8790  Z= 0.137
  Angle     :  0.594   6.900  12003  Z= 0.308
  Chirality :  0.045   0.206   1381
  Planarity :  0.004   0.078   1539
  Dihedral  :  4.743  36.905   1235
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.57 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 27.94 %
    Favored  : 65.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.25), residues: 1144
  helix:  0.63 (0.31), residues: 266
  sheet: -0.57 (0.29), residues: 366
  loop : -2.05 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  98 
 TYR   0.015   0.001   TYR A 261 
 PHE   0.019   0.001   PHE B 176 
 TRP   0.012   0.001   TRP H  33 
 HIS   0.002   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8784)
  covalent geometry    : angle       0.59379 (11991)
  SS BOND              : bond        0.00417 (    6)
  SS BOND              : angle       0.90287 (   12)
  hydrogen bonds       : bond        0.04111 (  293)
  hydrogen bonds       : angle       4.72792 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 96
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8048 (pp)
REVERT: A  166 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8413 (tt)
REVERT: A  209 MET cc_start: 0.7186 (tpp) cc_final: 0.6850 (tpp)
REVERT: A  213 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6405 (pm20)
REVERT: H    3 GLN cc_start: 0.7953 (mp10) cc_final: 0.7669 (mp10)
REVERT: H   98 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7223 (tmm-80)
REVERT: L   71 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6228 (m-80)
REVERT: L   92 ASN cc_start: 0.7524 (t0) cc_final: 0.7318 (t0)
  outliers start: 61
  outliers final: 44
  residues processed: 148
  average time/residue: 0.1066
  time to fit residues: 21.1921
Evaluate side-chains
  140 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 91
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   71 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 HIS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  359 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 50 optimal weight:   50.0000
   chunk 54 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.3980
   chunk 105 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0370
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.227532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.199472 restraints weight = 12340.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.195157 restraints weight = 27519.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.187711 restraints weight = 15223.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.187840 restraints weight = 16743.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.188443 restraints weight = 10364.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8790  Z= 0.115
  Angle     :  0.577   7.573  12003  Z= 0.299
  Chirality :  0.044   0.233   1381
  Planarity :  0.004   0.077   1539
  Dihedral  :  4.556  32.947   1235
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.17 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 29.64 %
    Favored  : 64.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1144
  helix:  0.74 (0.31), residues: 270
  sheet: -0.45 (0.29), residues: 364
  loop : -1.95 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.015   0.001   TYR A 261 
 PHE   0.022   0.001   PHE L 100 
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.000   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8784)
  covalent geometry    : angle       0.57712 (11991)
  SS BOND              : bond        0.00299 (    6)
  SS BOND              : angle       0.74522 (   12)
  hydrogen bonds       : bond        0.03658 (  293)
  hydrogen bonds       : angle       4.56762 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7870 (pp)
REVERT: A  166 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8446 (tt)
REVERT: A  209 MET cc_start: 0.7153 (tpp) cc_final: 0.6826 (tpp)
REVERT: A  213 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6372 (pm20)
REVERT: H    3 GLN cc_start: 0.7880 (mp10) cc_final: 0.7615 (mp10)
REVERT: H   98 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6828 (tmm-80)
REVERT: L   71 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.6090 (m-80)
REVERT: L   92 ASN cc_start: 0.7450 (t0) cc_final: 0.7243 (t0)
REVERT: B  358 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7002 (tpp)
  outliers start: 52
  outliers final: 37
  residues processed: 136
  average time/residue: 0.0977
  time to fit residues: 18.4397
Evaluate side-chains
  133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 90
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   71 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 HIS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 108 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    4.9990
   chunk 80 optimal weight:    0.3980
   chunk 110 optimal weight:    0.0050
   chunk 23 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.229084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.202896 restraints weight = 12172.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.193526 restraints weight = 25585.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.188995 restraints weight = 16683.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.188081 restraints weight = 17879.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.188952 restraints weight = 11732.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064   8790  Z= 0.106
  Angle     :  0.569   8.050  12003  Z= 0.294
  Chirality :  0.044   0.280   1381
  Planarity :  0.004   0.076   1539
  Dihedral  :  4.358  28.048   1235
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.34 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 29.64 %
    Favored  : 64.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.25), residues: 1144
  helix:  0.87 (0.31), residues: 270
  sheet: -0.44 (0.29), residues: 366
  loop : -1.90 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 187 
 TYR   0.016   0.001   TYR A 261 
 PHE   0.025   0.001   PHE L 100 
 TRP   0.008   0.001   TRP H  33 
 HIS   0.002   0.000   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8784)
  covalent geometry    : angle       0.56868 (11991)
  SS BOND              : bond        0.00314 (    6)
  SS BOND              : angle       0.69030 (   12)
  hydrogen bonds       : bond        0.03379 (  293)
  hydrogen bonds       : angle       4.46445 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 100
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7732 (pp)
REVERT: A  166 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8355 (tt)
REVERT: A  209 MET cc_start: 0.7069 (tpp) cc_final: 0.6764 (tpp)
REVERT: A  213 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6280 (pm20)
REVERT: H    3 GLN cc_start: 0.7831 (mp10) cc_final: 0.7568 (mp10)
REVERT: L   71 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6073 (m-80)
REVERT: L   92 ASN cc_start: 0.7435 (t0) cc_final: 0.7223 (t0)
REVERT: B  158 LEU cc_start: 0.8406 (tt) cc_final: 0.8190 (tt)
REVERT: B  358 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6946 (tpp)
REVERT: B  365 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6829 (pp)
  outliers start: 54
  outliers final: 39
  residues processed: 146
  average time/residue: 0.0919
  time to fit residues: 18.9009
Evaluate side-chains
  141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 96
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   71 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 HIS
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  365 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 30 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.225169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.196418 restraints weight = 12164.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.194391 restraints weight = 28132.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.190266 restraints weight = 13588.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.190394 restraints weight = 12688.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.190440 restraints weight = 9440.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8790  Z= 0.160
  Angle     :  0.621   8.634  12003  Z= 0.322
  Chirality :  0.046   0.261   1381
  Planarity :  0.005   0.077   1539
  Dihedral  :  4.547  30.112   1235
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.22 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 29.07 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1144
  helix:  0.83 (0.31), residues: 268
  sheet: -0.52 (0.29), residues: 370
  loop : -1.95 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 187 
 TYR   0.015   0.001   TYR A 261 
 PHE   0.032   0.002   PHE L 100 
 TRP   0.014   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8784)
  covalent geometry    : angle       0.62112 (11991)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       0.92200 (   12)
  hydrogen bonds       : bond        0.04126 (  293)
  hydrogen bonds       : angle       4.58289 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 95
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7986 (pp)
REVERT: A  133 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7371 (mt)
REVERT: A  166 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (tt)
REVERT: A  209 MET cc_start: 0.7220 (tpp) cc_final: 0.6900 (tpp)
REVERT: A  213 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6529 (pm20)
REVERT: H    3 GLN cc_start: 0.7831 (mp10) cc_final: 0.7591 (mp10)
REVERT: H  140 LYS cc_start: 0.4947 (tppt) cc_final: 0.4143 (tppt)
REVERT: L   71 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.5993 (m-80)
REVERT: L   92 ASN cc_start: 0.7407 (t0) cc_final: 0.7187 (t0)
REVERT: B  307 MET cc_start: 0.7554 (ttt) cc_final: 0.7184 (ttt)
REVERT: B  358 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7040 (tpp)
REVERT: B  365 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7002 (pp)
  outliers start: 56
  outliers final: 45
  residues processed: 142
  average time/residue: 0.0953
  time to fit residues: 18.8085
Evaluate side-chains
  146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 94
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   71 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 HIS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  365 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 90 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.224049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.194407 restraints weight = 12228.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.193378 restraints weight = 28922.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.189417 restraints weight = 13322.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.189444 restraints weight = 11821.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.189767 restraints weight = 9058.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8790  Z= 0.143
  Angle     :  0.612   8.303  12003  Z= 0.317
  Chirality :  0.045   0.250   1381
  Planarity :  0.005   0.076   1539
  Dihedral  :  4.556  30.514   1235
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.13 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 29.64 %
    Favored  : 64.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1144
  helix:  0.78 (0.31), residues: 269
  sheet: -0.47 (0.29), residues: 367
  loop : -1.96 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.015   0.001   TYR A 261 
 PHE   0.026   0.001   PHE L 100 
 TRP   0.012   0.001   TRP H  33 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8784)
  covalent geometry    : angle       0.61186 (11991)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       0.83865 (   12)
  hydrogen bonds       : bond        0.03906 (  293)
  hydrogen bonds       : angle       4.54964 (  834)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 96
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7962 (pp)
REVERT: A  133 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7330 (mt)
REVERT: A  166 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8409 (tt)
REVERT: A  209 MET cc_start: 0.7219 (tpp) cc_final: 0.6893 (tpp)
REVERT: A  213 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6435 (pm20)
REVERT: H    3 GLN cc_start: 0.7848 (mp10) cc_final: 0.7613 (mp10)
REVERT: H  140 LYS cc_start: 0.5010 (tppt) cc_final: 0.4018 (tppt)
REVERT: L   71 PHE cc_start: 0.6309 (OUTLIER) cc_final: 0.6027 (m-80)
REVERT: L   92 ASN cc_start: 0.7442 (t0) cc_final: 0.7228 (t0)
REVERT: B  358 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7007 (tpp)
REVERT: B  365 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6973 (pp)
  outliers start: 54
  outliers final: 44
  residues processed: 143
  average time/residue: 0.0921
  time to fit residues: 18.4417
Evaluate side-chains
  146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 95
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  177 GLN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  252 ARG
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  135 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   71 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  182 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 HIS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  359 HIS
Chi-restraints excluded: chain B residue  365 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 55 optimal weight:    0.2980
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 75 optimal weight:   40.0000
   chunk 38 optimal weight:   20.0000
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
L 139 ASN
L 191 HIS
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.204230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.182020 restraints weight = 11718.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.175865 restraints weight = 22035.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172320 restraints weight = 24828.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.171766 restraints weight = 25254.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.170924 restraints weight = 19353.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8790  Z= 0.225
  Angle     :  0.698   8.112  12003  Z= 0.364
  Chirality :  0.048   0.249   1381
  Planarity :  0.005   0.074   1539
  Dihedral  :  4.957  34.932   1235
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.27 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 28.51 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.25), residues: 1144
  helix:  0.52 (0.31), residues: 265
  sheet: -0.66 (0.28), residues: 378
  loop : -2.05 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.017   0.002   TYR L  49 
 PHE   0.027   0.002   PHE L 100 
 TRP   0.019   0.002   TRP H  33 
 HIS   0.004   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 8784)
  covalent geometry    : angle       0.69698 (11991)
  SS BOND              : bond        0.00364 (    6)
  SS BOND              : angle       1.21066 (   12)
  hydrogen bonds       : bond        0.05058 (  293)
  hydrogen bonds       : angle       4.82836 (  834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1517.26 seconds
wall clock time: 27 minutes 0.91 seconds (1620.91 seconds total)