Starting phenix.real_space_refine
on Thu Mar 13 05:50:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vuv_43541/03_2025/8vuv_43541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vuv_43541/03_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_43541/03_2025/8vuv_43541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vuv_43541/03_2025/8vuv_43541.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vuv_43541/03_2025/8vuv_43541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vuv_43541/03_2025/8vuv_43541.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4}
          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, 'ARG:plan': 1, 'GLU: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: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 109
  Time building chain proxies: 6.30, per 1000 atoms: 0.73
  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: 2.11
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.05
  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: 2.39

  Time building geometry restraints manager: 2.51 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:             5.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.500
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.770
-------------------------------------------------------------------------------
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   8784  Z= 0.210
  Angle     :  0.628  11.075  11991  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 : 8.86
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (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
 TRP   0.011   0.001   TRP L  98 
 HIS   0.002   0.001   HIS A 280 
 PHE   0.020   0.001   PHE L 100 
 TYR   0.009   0.001   TYR H  94 
 ARG   0.010   0.000   ARG B 187 

*********************** 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  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: L   92 ASN cc_start: 0.6900 (t0) cc_final: 0.6669 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.2416
  time to fit residues: 34.0303
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  : 0.978 
-------------------------------------------------------------------------------
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 96 optimal weight:    0.0270
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   chunk 58 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.4667 r_free = 0.4667 target = 0.231215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.204349 restraints weight = 12232.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.201763 restraints weight = 29347.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.199256 restraints weight = 14841.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.0794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8784  Z= 0.186
  Angle     :  0.596   8.860  11991  Z= 0.310
  Chirality :  0.044   0.205   1381
  Planarity :  0.005   0.080   1539
  Dihedral  :  4.491  29.279   1237
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.69 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 29.86 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.25), residues: 1144
  helix:  0.77 (0.31), residues: 267
  sheet: -0.45 (0.28), residues: 366
  loop : -1.86 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  33 
 HIS   0.002   0.000   HIS A 293 
 PHE   0.010   0.001   PHE L 100 
 TYR   0.013   0.001   TYR A 261 
 ARG   0.008   0.000   ARG B 187 

*********************** 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
  135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (tt)
REVERT: L   92 ASN cc_start: 0.7288 (t0) cc_final: 0.7073 (t0)
  outliers start: 36
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1975
  time to fit residues: 35.3234
Evaluate side-chains
  109 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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   79 CYS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  326 MET
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   68 VAL
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain B residue  157 MET
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 51 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0970
   chunk 81 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 107 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 101 optimal weight:    1.9990
   chunk 54 optimal weight:   40.0000
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4620 r_free = 0.4620 target = 0.226255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.194587 restraints weight = 12342.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.191918 restraints weight = 28965.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.185132 restraints weight = 13354.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8784  Z= 0.212
  Angle     :  0.591   8.792  11991  Z= 0.306
  Chirality :  0.044   0.205   1381
  Planarity :  0.005   0.080   1539
  Dihedral  :  4.463  30.304   1235
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.13 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.73 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.25), residues: 1144
  helix:  0.79 (0.31), residues: 266
  sheet: -0.40 (0.29), residues: 365
  loop : -1.89 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.019   0.001   PHE L 100 
 TYR   0.014   0.001   TYR A 261 
 ARG   0.007   0.000   ARG B 187 

*********************** 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
  140 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 96
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8297 (tt)
REVERT: A  213 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6482 (pm20)
REVERT: L   92 ASN cc_start: 0.7486 (t0) cc_final: 0.7279 (t0)
REVERT: B  358 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6845 (tpp)
  outliers start: 44
  outliers final: 31
  residues processed: 132
  average time/residue: 0.2058
  time to fit residues: 38.9103
Evaluate side-chains
  128 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
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  254 ILE
Chi-restraints excluded: chain A residue  296 LEU
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   73 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   51 LYS
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  280 VAL
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 70 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 92 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:   30.0000
   chunk 14 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4625 r_free = 0.4625 target = 0.226394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.195849 restraints weight = 12246.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.196762 restraints weight = 28388.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.193240 restraints weight = 13926.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8784  Z= 0.241
  Angle     :  0.596   7.672  11991  Z= 0.309
  Chirality :  0.045   0.204   1381
  Planarity :  0.005   0.080   1539
  Dihedral  :  4.569  31.857   1235
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.48 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 27.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.25), residues: 1144
  helix:  0.76 (0.31), residues: 266
  sheet: -0.42 (0.29), residues: 365
  loop : -1.92 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.012   0.001   PHE B 176 
 TYR   0.014   0.001   TYR L  49 
 ARG   0.004   0.000   ARG B 187 

*********************** 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
  156 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 95
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8023 (pp)
REVERT: A  162 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7907 (m90)
REVERT: A  166 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8375 (tt)
REVERT: A  213 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6423 (pm20)
REVERT: A  346 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8353 (tpt-90)
REVERT: H   98 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6885 (tmm-80)
REVERT: L   92 ASN cc_start: 0.7366 (t0) cc_final: 0.7141 (t0)
REVERT: B  358 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6961 (tpp)
REVERT: B  365 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7096 (pp)
  outliers start: 61
  outliers final: 39
  residues processed: 147
  average time/residue: 0.2525
  time to fit residues: 50.9621
Evaluate side-chains
  140 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 93
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
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   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  162 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
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  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   98 ARG
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   97 VAL
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  273 PHE
Chi-restraints excluded: chain B residue  280 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
Chi-restraints excluded: chain B residue  365 ILE
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 26 optimal weight:    0.9980
   chunk 52 optimal weight:   40.0000
   chunk 78 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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**
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.225362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.193655 restraints weight = 12121.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.194038 restraints weight = 31852.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.193761 restraints weight = 17697.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8784  Z= 0.260
  Angle     :  0.607   7.718  11991  Z= 0.315
  Chirality :  0.045   0.205   1381
  Planarity :  0.005   0.079   1539
  Dihedral  :  4.643  32.589   1235
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.39 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 26.13 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.25), residues: 1144
  helix:  0.70 (0.31), residues: 268
  sheet: -0.44 (0.29), residues: 364
  loop : -1.93 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.022   0.001   PHE L 100 
 TYR   0.014   0.001   TYR A 261 
 ARG   0.003   0.000   ARG B 187 

*********************** 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
  161 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 93
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8099 (pp)
REVERT: A  162 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.8002 (m90)
REVERT: A  166 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8359 (tt)
REVERT: A  213 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6411 (pm20)
REVERT: A  346 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8269 (tpt-90)
REVERT: L   92 ASN cc_start: 0.7386 (t0) cc_final: 0.7159 (t0)
REVERT: B  358 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6989 (tpp)
  outliers start: 68
  outliers final: 46
  residues processed: 149
  average time/residue: 0.2270
  time to fit residues: 47.2118
Evaluate side-chains
  144 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 92
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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   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  167 VAL
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  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 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  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   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   68 VAL
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  195 VAL
Chi-restraints excluded: chain B residue  273 PHE
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  300 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  366 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 75 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H 196 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 139 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.205087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.185731 restraints weight = 11648.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.180395 restraints weight = 19422.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173774 restraints weight = 22246.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8784  Z= 0.371
  Angle     :  0.676   7.818  11991  Z= 0.354
  Chirality :  0.048   0.209   1381
  Planarity :  0.005   0.078   1539
  Dihedral  :  5.039  38.297   1235
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.00 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  7.92 %
    Allowed  : 26.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.25), residues: 1144
  helix:  0.52 (0.31), residues: 264
  sheet: -0.56 (0.29), residues: 365
  loop : -2.06 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H  33 
 HIS   0.006   0.001   HIS A 134 
 PHE   0.023   0.002   PHE L 100 
 TYR   0.017   0.002   TYR L  49 
 ARG   0.003   0.000   ARG B 187 

*********************** 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
  164 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 94
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8296 (pp)
REVERT: A  119 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8251 (mp)
REVERT: A  166 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8395 (tt)
REVERT: A  213 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6685 (pm20)
REVERT: A  346 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8336 (tpt-90)
REVERT: H    3 GLN cc_start: 0.7853 (mp10) cc_final: 0.7622 (mp10)
REVERT: H   98 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7424 (tmm-80)
REVERT: L   92 ASN cc_start: 0.7379 (t0) cc_final: 0.7160 (t0)
REVERT: B  187 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.8112 (mmt90)
REVERT: B  358 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7038 (tpp)
  outliers start: 70
  outliers final: 47
  residues processed: 154
  average time/residue: 0.2556
  time to fit residues: 54.0478
Evaluate side-chains
  143 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 89
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
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   58 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
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  334 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  364 VAL
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   58 ILE
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain B residue   37 ILE
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  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  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  342 VAL
Chi-restraints excluded: chain B residue  343 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 56 optimal weight:   40.0000
   chunk 108 optimal weight:    0.0470
   chunk 15 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 111 optimal weight:    0.5980
   chunk 50 optimal weight:    9.9990
   chunk 91 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.209916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.186758 restraints weight = 11702.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181118 restraints weight = 25037.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178477 restraints weight = 24458.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8784  Z= 0.189
  Angle     :  0.591   7.731  11991  Z= 0.306
  Chirality :  0.044   0.205   1381
  Planarity :  0.004   0.077   1539
  Dihedral  :  4.658  34.140   1235
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.95 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 28.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.25), residues: 1144
  helix:  0.71 (0.31), residues: 267
  sheet: -0.48 (0.29), residues: 364
  loop : -1.97 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.000   HIS A 293 
 PHE   0.018   0.001   PHE L 100 
 TYR   0.010   0.001   TYR L  36 
 ARG   0.002   0.000   ARG B 187 

*********************** 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
  144 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 91
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (pp)
REVERT: A  166 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: A  213 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6338 (pm20)
REVERT: A  346 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8421 (tpt-90)
REVERT: H    3 GLN cc_start: 0.7784 (mp10) cc_final: 0.7569 (mp10)
REVERT: H   98 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7051 (tmm-80)
REVERT: L   92 ASN cc_start: 0.7224 (t0) cc_final: 0.7000 (t0)
REVERT: B  158 LEU cc_start: 0.8374 (tt) cc_final: 0.8161 (tt)
REVERT: B  306 ASP cc_start: 0.7396 (t70) cc_final: 0.7038 (t0)
REVERT: B  358 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6911 (tpp)
  outliers start: 53
  outliers final: 34
  residues processed: 135
  average time/residue: 0.2089
  time to fit residues: 38.9614
Evaluate side-chains
  129 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 89
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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   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  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  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   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   85 VAL
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  173 THR
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  335 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4336 r_free = 0.4336 target = 0.208158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.185495 restraints weight = 11754.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.179138 restraints weight = 24319.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.176970 restraints weight = 26292.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8784  Z= 0.250
  Angle     :  0.613   7.981  11991  Z= 0.317
  Chirality :  0.045   0.205   1381
  Planarity :  0.004   0.077   1539
  Dihedral  :  4.684  34.417   1235
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.92 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 29.30 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.25), residues: 1144
  helix:  0.75 (0.31), residues: 265
  sheet: -0.48 (0.29), residues: 364
  loop : -1.97 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  33 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.017   0.001   PHE L 100 
 TYR   0.013   0.001   TYR L  49 
 ARG   0.002   0.000   ARG B 187 

*********************** 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
  140 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 89
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8141 (pp)
REVERT: A  133 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7226 (mt)
REVERT: A  166 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8395 (tt)
REVERT: A  213 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6545 (pm20)
REVERT: H    3 GLN cc_start: 0.7788 (mp10) cc_final: 0.7573 (mp10)
REVERT: H   98 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7184 (tmm-80)
REVERT: L   92 ASN cc_start: 0.7250 (t0) cc_final: 0.7019 (t0)
REVERT: B  168 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6036 (pt)
REVERT: B  306 ASP cc_start: 0.7425 (t70) cc_final: 0.7046 (t0)
REVERT: B  358 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6954 (tpp)
  outliers start: 51
  outliers final: 40
  residues processed: 133
  average time/residue: 0.2253
  time to fit residues: 41.0441
Evaluate side-chains
  135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 88
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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   58 ILE
Chi-restraints excluded: chain A residue   60 LEU
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  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  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   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   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  108 ILE
Chi-restraints excluded: chain B residue  157 MET
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  280 VAL
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  335 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0020
   chunk 45 optimal weight:    0.6980
   chunk 48 optimal weight:   50.0000
   chunk 77 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7188

-------------------------------------------------------------------------------
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 = 0.4355 r_free = 0.4355 target = 0.210224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.189096 restraints weight = 11649.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.183019 restraints weight = 20671.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.179857 restraints weight = 23846.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8784  Z= 0.205
  Angle     :  0.596   8.526  11991  Z= 0.307
  Chirality :  0.045   0.257   1381
  Planarity :  0.004   0.076   1539
  Dihedral  :  4.579  33.368   1235
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.87 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.52 %
    Favored  : 65.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.25), residues: 1144
  helix:  0.78 (0.31), residues: 268
  sheet: -0.43 (0.29), residues: 364
  loop : -1.92 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS A 293 
 PHE   0.016   0.001   PHE B 176 
 TYR   0.010   0.001   TYR L  49 
 ARG   0.004   0.000   ARG B 187 

*********************** 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
  143 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 95
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (pp)
REVERT: A  133 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7178 (mt)
REVERT: A  166 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (tt)
REVERT: A  213 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6421 (pm20)
REVERT: H    3 GLN cc_start: 0.7839 (mp10) cc_final: 0.7594 (mp10)
REVERT: H   98 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7095 (tmm-80)
REVERT: H  140 LYS cc_start: 0.4592 (tppt) cc_final: 0.3845 (tppt)
REVERT: L   92 ASN cc_start: 0.7324 (t0) cc_final: 0.7093 (t0)
REVERT: B  158 LEU cc_start: 0.8396 (tt) cc_final: 0.8152 (tt)
REVERT: B  306 ASP cc_start: 0.7507 (t70) cc_final: 0.7151 (t0)
REVERT: B  358 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.6941 (tpp)
  outliers start: 48
  outliers final: 38
  residues processed: 137
  average time/residue: 0.2242
  time to fit residues: 41.9216
Evaluate side-chains
  133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 89
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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   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  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  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   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   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  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  280 VAL
Chi-restraints excluded: chain B residue  287 TYR
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  335 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:   40.0000
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0470
   chunk 76 optimal weight:   40.0000
   chunk 92 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.4563 r_free = 0.4563 target = 0.220934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.189015 restraints weight = 12310.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.188156 restraints weight = 29311.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.184472 restraints weight = 14212.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8784  Z= 0.190
  Angle     :  0.598   8.327  11991  Z= 0.307
  Chirality :  0.045   0.277   1381
  Planarity :  0.004   0.075   1539
  Dihedral  :  4.446  30.761   1235
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.22 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 29.64 %
    Favored  : 65.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.25), residues: 1144
  helix:  0.83 (0.31), residues: 271
  sheet: -0.44 (0.29), residues: 370
  loop : -1.89 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.000   HIS A 293 
 PHE   0.016   0.001   PHE B 176 
 TYR   0.017   0.001   TYR A 261 
 ARG   0.004   0.000   ARG B 187 

********************** 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
  144 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 97
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7863 (pp)
REVERT: A  133 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7221 (mt)
REVERT: A  166 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8369 (tt)
REVERT: A  213 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6379 (pm20)
REVERT: H    3 GLN cc_start: 0.7868 (mp10) cc_final: 0.7572 (mp10)
REVERT: H   98 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6888 (tmm-80)
REVERT: H  140 LYS cc_start: 0.5144 (tppt) cc_final: 0.4334 (tppt)
REVERT: L   92 ASN cc_start: 0.7458 (t0) cc_final: 0.7248 (t0)
REVERT: B  158 LEU cc_start: 0.8388 (tt) cc_final: 0.8171 (tt)
REVERT: B  168 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6104 (pt)
REVERT: B  306 ASP cc_start: 0.7661 (t70) cc_final: 0.7295 (t0)
REVERT: B  358 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.6892 (tpp)
  outliers start: 47
  outliers final: 39
  residues processed: 140
  average time/residue: 0.2065
  time to fit residues: 40.7233
Evaluate side-chains
  137 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 91
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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   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  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  334 VAL
Chi-restraints excluded: chain A residue  364 VAL
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   58 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   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  168 ILE
Chi-restraints excluded: chain B residue  173 THR
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  299 ILE
Chi-restraints excluded: chain B residue  335 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 71 optimal weight:   30.0000
   chunk 106 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 218 ASN ** 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 = 0.4601 r_free = 0.4601 target = 0.224319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.190324 restraints weight = 12231.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.182876 restraints weight = 21567.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.180973 restraints weight = 16777.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8784  Z= 0.233
  Angle     :  0.615   8.072  11991  Z= 0.318
  Chirality :  0.045   0.258   1381
  Planarity :  0.005   0.075   1539
  Dihedral  :  4.521  31.712   1235
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.22 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 29.19 %
    Favored  : 64.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.25), residues: 1144
  helix:  0.74 (0.31), residues: 269
  sheet: -0.47 (0.29), residues: 372
  loop : -1.93 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  33 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.015   0.001   PHE B 176 
 TYR   0.015   0.001   TYR A 261 
 ARG   0.003   0.000   ARG B 187 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2769.00 seconds
wall clock time: 49 minutes 54.36 seconds (2994.36 seconds total)