Starting phenix.real_space_refine
on Thu May 22 17:04:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8adg_15362/05_2025/8adg_15362.cif"
  }
  resolution = 3.0
  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=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7440      2.51       5
     N    2019      2.21       5
     O    2317      1.98       5
     H   11383      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 23191
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 12167
          Classifications: {'peptide': 787}
          Link IDs: {'PTRANS': 29, 'TRANS': 757}
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 5393
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 11, 'TRANS': 349}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 845
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3348
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1292
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 146
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 10.50, per 1000 atoms: 0.45
  Number of scatterers: 23191
  At special positions: 0
  Unit cell: (97.75, 133.45, 125.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2317      8.00
     N    2019      7.00
     C    7440      6.00
     H   11383      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 5.72
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2756

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 17 sheets defined
      24.2% alpha, 30.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
      removed outlier: 4.019A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.795A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.042A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 497 through 500
      removed outlier: 3.980A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 500'
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 3.607A  pdb=" N   TYR A 550 " --> pdb=" O   TRP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.616A  pdb=" N   GLY A 695 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'C' and resid 31 through 39
      removed outlier: 4.039A  pdb=" N   VAL C  35 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.080A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.502A  pdb=" N   GLU D 187 " --> pdb=" O   GLU D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.669A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.659A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 242
      removed outlier: 3.529A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 46
      removed outlier: 3.815A  pdb=" N   ILE E  46 " --> pdb=" O   VAL E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 7.357A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   GLU A  32 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.428A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.460A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 8.820A  pdb=" N   SER B 193 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL A 245 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 270
      removed outlier: 6.251A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.623A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ALA A 343 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN A 276 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 270
      removed outlier: 6.251A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.623A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.715A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 5
      removed outlier: 3.519A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50
      removed outlier: 5.157A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.610A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 117
      removed outlier: 6.245A  pdb=" N   GLY B 114 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   GLY B 125 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.765A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202
      removed outlier: 6.733A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.517A  pdb=" N   ALA B 269 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.543A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.807A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 4.036A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    525 hydrogen bonds defined for protein.
    1467 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: 10.01

  Time building geometry restraints manager: 6.85 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11339
        1.03 -     1.23: 59
        1.23 -     1.42: 5210
        1.42 -     1.61: 6781
        1.61 -     1.81: 62
  Bond restraints: 23451
  Sorted by residual:
  bond pdb=" CG  PRO B  34 "
       pdb=" CD  PRO B  34 "
    ideal  model  delta    sigma   weight residual
    1.503  1.047  0.456 3.40e-02 8.65e+02 1.80e+02
  bond pdb=" C   UX8 F   3 "
       pdb=" O   UX8 F   3 "
    ideal  model  delta    sigma   weight residual
    1.231  1.395 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" CZ2 TRP F   1 "
       pdb=" HZ2 TRP F   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.090 -0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" CZ3 UX8 F   3 "
       pdb=" HZ3 UX8 F   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CD1 TRP F   7 "
       pdb=" HD1 TRP F   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 23446 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.92: 42151
        4.92 -     9.83: 11
        9.83 -    14.75: 5
       14.75 -    19.67: 3
       19.67 -    24.59: 1
  Bond angle restraints: 42171
  Sorted by residual:
  angle pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     103.20   78.61   24.59 1.50e+00 4.44e-01 2.69e+02
  angle pdb=" CA  PRO B  34 "
        pdb=" CB  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     104.50   87.73   16.77 1.90e+00 2.77e-01 7.79e+01
  angle pdb=" CA  PRO B  34 "
        pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     112.00  100.72   11.28 1.40e+00 5.10e-01 6.49e+01
  angle pdb=" CA  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     109.00   90.49   18.51 3.00e+00 1.11e-01 3.81e+01
  angle pdb=" CG  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     108.00   90.51   17.49 3.00e+00 1.11e-01 3.40e+01
  ... (remaining 42166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 10129
       17.96 -    35.91: 726
       35.91 -    53.87: 198
       53.87 -    71.82: 46
       71.82 -    89.78: 14
  Dihedral angle restraints: 11113
    sinusoidal: 5987
      harmonic: 5126
  Sorted by residual:
  dihedral pdb=" CD2 TRP F   1 "
           pdb=" CE2 TRP F   1 "
           pdb=" CZ2 TRP F   1 "
           pdb=" HZ2 TRP F   1 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.33  -54.67     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.25   45.25     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" CA  LEU A 699 "
           pdb=" C   LEU A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 11110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 994
       0.029 -    0.058: 521
       0.058 -    0.087: 115
       0.087 -    0.116: 109
       0.116 -    0.145: 44
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CA  ILE C  67 "
            pdb=" N   ILE C  67 "
            pdb=" C   ILE C  67 "
            pdb=" CB  ILE C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE E 104 "
            pdb=" N   ILE E 104 "
            pdb=" C   ILE E 104 "
            pdb=" CB  ILE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 1780 not shown)

  Planarity restraints: 3593
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F   1 "   -0.129 2.00e-02 2.50e+03   1.84e-01 1.27e+03
        pdb=" CG  TRP F   1 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP F   1 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP F   1 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP F   1 "    0.107 2.00e-02 2.50e+03
        pdb=" CE2 TRP F   1 "    0.108 2.00e-02 2.50e+03
        pdb=" CE3 TRP F   1 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F   1 "    0.183 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F   1 "    0.068 2.00e-02 2.50e+03
        pdb=" CH2 TRP F   1 "    0.159 2.00e-02 2.50e+03
        pdb=" HD1 TRP F   1 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE1 TRP F   1 "    0.155 2.00e-02 2.50e+03
        pdb=" HE3 TRP F   1 "   -0.078 2.00e-02 2.50e+03
        pdb=" HZ2 TRP F   1 "   -0.608 2.00e-02 2.50e+03
        pdb=" HZ3 TRP F   1 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "   -0.034 2.00e-02 2.50e+03   2.19e-02 1.92e+01
        pdb=" CG  TRP A 546 "    0.074 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "   -0.011 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 546 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 546 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 546 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  33 "   -0.042 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO B  34 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  34 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  34 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 3590 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 591
        2.15 -     2.76: 42757
        2.76 -     3.37: 61231
        3.37 -     3.99: 81598
        3.99 -     4.60: 128113
  Nonbonded interactions: 314290
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  38 "
            pdb=" H   GLU C  39 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" OD1 ASN E  96 "
            pdb=" H   SER E  98 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" O   ARG A 661 "
            pdb=" HG  SER A 769 "
     model   vdw
     1.614 2.450
  nonbonded pdb="HE21 GLN B 319 "
            pdb=" O   GLY B 354 "
     model   vdw
     1.620 2.450
  ... (remaining 314285 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.370
  Extract box with map and model:          0.880
  Check model and map are aligned:         0.180
  Set scattering table:                    0.200
  Process input model:                     49.320
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:13.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.006   0.456  12071  Z= 0.232
  Angle     :  0.622  24.587  16405  Z= 0.351
  Chirality :  0.044   0.145   1783
  Planarity :  0.004   0.058   2158
  Dihedral  : 14.028  89.781   4366
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.21), residues: 1487
  helix:  2.32 (0.29), residues: 326
  sheet:  0.30 (0.25), residues: 445
  loop : -0.98 (0.21), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP A 546 
 HIS   0.014   0.001   HIS D 102 
 PHE   0.015   0.001   PHE A 791 
 TYR   0.015   0.001   TYR A 794 
 ARG   0.010   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08422 (  521)
  hydrogen bonds       : angle       4.92835 ( 1467)
  SS BOND              : bond        0.00403 (    1)
  SS BOND              : angle       1.81828 (    2)
  covalent geometry    : bond        0.00603 (12068)
  covalent geometry    : angle       0.62218 (16403)
  Misc. bond           : bond        0.00139 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  520 ASN cc_start: 0.7562 (t0) cc_final: 0.7288 (t0)
REVERT: B  268 THR cc_start: 0.8547 (t) cc_final: 0.8294 (m)
REVERT: C   41 TYR cc_start: 0.6295 (p90) cc_final: 0.6046 (p90)
REVERT: D   93 ASP cc_start: 0.8091 (m-30) cc_final: 0.7728 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 2.0887
  time to fit residues: 310.6174
Evaluate side-chains
  110 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0870
   chunk 85 optimal weight:    3.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    1.1762

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 561 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.127212 restraints weight = 35147.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.02
r_work: 0.3239 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.0595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12071  Z= 0.151
  Angle     :  0.519   7.061  16405  Z= 0.277
  Chirality :  0.043   0.147   1783
  Planarity :  0.004   0.041   2158
  Dihedral  :  4.209  19.885   1651
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  5.78 %
    Favored  : 93.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.22), residues: 1487
  helix:  2.34 (0.28), residues: 327
  sheet:  0.39 (0.25), residues: 439
  loop : -0.96 (0.22), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 546 
 HIS   0.006   0.001   HIS D 102 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.010   0.001   TYR D  79 
 ARG   0.007   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04614 (  521)
  hydrogen bonds       : angle       4.62455 ( 1467)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       1.61342 (    2)
  covalent geometry    : bond        0.00357 (12068)
  covalent geometry    : angle       0.51917 (16403)
  Misc. bond           : bond        0.00447 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6619 (mm-30)
REVERT: A  286 GLN cc_start: 0.7443 (mp10) cc_final: 0.6498 (tm130)
REVERT: A  520 ASN cc_start: 0.8049 (t0) cc_final: 0.7559 (t0)
REVERT: B   70 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (t0)
REVERT: B  268 THR cc_start: 0.8508 (t) cc_final: 0.8243 (m)
REVERT: C   41 TYR cc_start: 0.6789 (p90) cc_final: 0.6152 (p90)
REVERT: D   93 ASP cc_start: 0.8212 (m-30) cc_final: 0.7733 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 119
  average time/residue: 2.1922
  time to fit residues: 290.1833
Evaluate side-chains
  115 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   42 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 108 optimal weight:    0.5980
   chunk 144 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 GLN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.173446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.128991 restraints weight = 35061.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.06
r_work: 0.3249 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12071  Z= 0.122
  Angle     :  0.483   6.723  16405  Z= 0.257
  Chirality :  0.042   0.145   1783
  Planarity :  0.004   0.041   2158
  Dihedral  :  4.089  18.113   1651
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  7.36 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.22), residues: 1487
  helix:  2.50 (0.29), residues: 327
  sheet:  0.37 (0.25), residues: 441
  loop : -0.93 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.006   0.001   HIS B 347 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.012   0.001   TYR D  79 
 ARG   0.007   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  521)
  hydrogen bonds       : angle       4.44916 ( 1467)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       1.59367 (    2)
  covalent geometry    : bond        0.00284 (12068)
  covalent geometry    : angle       0.48223 (16403)
  Misc. bond           : bond        0.00455 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 1.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ASP cc_start: 0.8300 (p0) cc_final: 0.8095 (p0)
REVERT: A  286 GLN cc_start: 0.7370 (mp10) cc_final: 0.6405 (tm130)
REVERT: A  520 ASN cc_start: 0.7947 (t0) cc_final: 0.7398 (t0)
REVERT: A  614 ASP cc_start: 0.8330 (m-30) cc_final: 0.8023 (m-30)
REVERT: B   70 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8142 (t0)
REVERT: B  266 ASN cc_start: 0.6858 (p0) cc_final: 0.6496 (p0)
REVERT: B  268 THR cc_start: 0.8491 (t) cc_final: 0.8167 (m)
REVERT: C   41 TYR cc_start: 0.6778 (p90) cc_final: 0.6246 (p90)
REVERT: D   93 ASP cc_start: 0.8206 (m-30) cc_final: 0.7733 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 124
  average time/residue: 2.1309
  time to fit residues: 293.6254
Evaluate side-chains
  120 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 1.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 110 optimal weight:    3.9990
   chunk 141 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 101 optimal weight:    0.5980
   chunk 120 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.172833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.127499 restraints weight = 35349.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.12
r_work: 0.3248 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12071  Z= 0.106
  Angle     :  0.464   6.469  16405  Z= 0.246
  Chirality :  0.042   0.142   1783
  Planarity :  0.003   0.040   2158
  Dihedral  :  3.989  17.292   1651
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.47 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.22), residues: 1487
  helix:  2.66 (0.29), residues: 327
  sheet:  0.25 (0.24), residues: 459
  loop : -0.84 (0.22), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 348 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.010   0.001   TYR D  79 
 ARG   0.005   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03800 (  521)
  hydrogen bonds       : angle       4.35778 ( 1467)
  SS BOND              : bond        0.00260 (    1)
  SS BOND              : angle       1.49307 (    2)
  covalent geometry    : bond        0.00244 (12068)
  covalent geometry    : angle       0.46364 (16403)
  Misc. bond           : bond        0.00401 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 1.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7331 (mp10) cc_final: 0.6394 (tm130)
REVERT: A  520 ASN cc_start: 0.8015 (t0) cc_final: 0.7553 (t0)
REVERT: A  614 ASP cc_start: 0.8306 (m-30) cc_final: 0.7986 (m-30)
REVERT: B   70 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (t0)
REVERT: B  266 ASN cc_start: 0.6889 (p0) cc_final: 0.6469 (p0)
REVERT: B  268 THR cc_start: 0.8482 (t) cc_final: 0.8155 (m)
REVERT: C   41 TYR cc_start: 0.6765 (p90) cc_final: 0.6295 (p90)
REVERT: D   93 ASP cc_start: 0.8217 (m-30) cc_final: 0.7743 (m-30)
  outliers start: 16
  outliers final: 11
  residues processed: 120
  average time/residue: 2.0635
  time to fit residues: 275.1871
Evaluate side-chains
  118 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 144 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 359 GLN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.171351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.124366 restraints weight = 35580.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.15
r_work: 0.3200 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12071  Z= 0.200
  Angle     :  0.530   7.945  16405  Z= 0.282
  Chirality :  0.044   0.143   1783
  Planarity :  0.004   0.046   2158
  Dihedral  :  4.211  17.546   1651
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.11 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.22), residues: 1487
  helix:  2.31 (0.28), residues: 330
  sheet:  0.17 (0.24), residues: 447
  loop : -0.98 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 143 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.016   0.002   PHE A 791 
 TYR   0.011   0.001   TYR A 787 
 ARG   0.007   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 (  521)
  hydrogen bonds       : angle       4.49552 ( 1467)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       1.48683 (    2)
  covalent geometry    : bond        0.00487 (12068)
  covalent geometry    : angle       0.52930 (16403)
  Misc. bond           : bond        0.00410 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 1.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7298 (mp10) cc_final: 0.6308 (tm130)
REVERT: A  520 ASN cc_start: 0.8028 (t0) cc_final: 0.7533 (t0)
REVERT: A  614 ASP cc_start: 0.8329 (m-30) cc_final: 0.8070 (m-30)
REVERT: B   70 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (t0)
REVERT: B  268 THR cc_start: 0.8474 (t) cc_final: 0.8175 (m)
REVERT: C   41 TYR cc_start: 0.6836 (p90) cc_final: 0.6406 (p90)
REVERT: D   93 ASP cc_start: 0.8090 (m-30) cc_final: 0.7622 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 122
  average time/residue: 2.2519
  time to fit residues: 308.2706
Evaluate side-chains
  121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 359 GLN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.122918 restraints weight = 35312.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.14
r_work: 0.3189 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12071  Z= 0.196
  Angle     :  0.540   8.284  16405  Z= 0.288
  Chirality :  0.044   0.166   1783
  Planarity :  0.004   0.050   2158
  Dihedral  :  4.350  18.640   1651
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.06 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.21), residues: 1487
  helix:  2.10 (0.28), residues: 330
  sheet:  0.15 (0.25), residues: 441
  loop : -1.10 (0.21), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 143 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.017   0.002   PHE A 426 
 TYR   0.012   0.001   TYR A 754 
 ARG   0.011   0.001   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04766 (  521)
  hydrogen bonds       : angle       4.55910 ( 1467)
  SS BOND              : bond        0.00402 (    1)
  SS BOND              : angle       1.54908 (    2)
  covalent geometry    : bond        0.00474 (12068)
  covalent geometry    : angle       0.54001 (16403)
  Misc. bond           : bond        0.00415 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7280 (mp10) cc_final: 0.6335 (tm130)
REVERT: A  520 ASN cc_start: 0.8087 (t0) cc_final: 0.7634 (t0)
REVERT: A  614 ASP cc_start: 0.8346 (m-30) cc_final: 0.8088 (m-30)
REVERT: B   32 MET cc_start: 0.7130 (tpp) cc_final: 0.6929 (tpp)
REVERT: B   70 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8130 (t0)
REVERT: B  268 THR cc_start: 0.8462 (t) cc_final: 0.8200 (m)
REVERT: C   41 TYR cc_start: 0.6706 (p90) cc_final: 0.6161 (p90)
REVERT: C   76 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7665 (p)
REVERT: D   93 ASP cc_start: 0.8230 (m-30) cc_final: 0.7763 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 124
  average time/residue: 2.1709
  time to fit residues: 297.3252
Evaluate side-chains
  123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  359 GLN
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.171863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.126205 restraints weight = 35386.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.07
r_work: 0.3221 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12071  Z= 0.129
  Angle     :  0.500   7.570  16405  Z= 0.267
  Chirality :  0.043   0.149   1783
  Planarity :  0.004   0.050   2158
  Dihedral  :  4.247  17.365   1651
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.69 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.21), residues: 1487
  helix:  2.41 (0.28), residues: 326
  sheet:  0.19 (0.24), residues: 443
  loop : -1.03 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 348 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 426 
 TYR   0.012   0.001   TYR D  79 
 ARG   0.010   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  521)
  hydrogen bonds       : angle       4.46855 ( 1467)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       1.32485 (    2)
  covalent geometry    : bond        0.00300 (12068)
  covalent geometry    : angle       0.50015 (16403)
  Misc. bond           : bond        0.00380 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7238 (mp10) cc_final: 0.6287 (tm130)
REVERT: A  520 ASN cc_start: 0.8013 (t0) cc_final: 0.7510 (t0)
REVERT: A  614 ASP cc_start: 0.8301 (m-30) cc_final: 0.8025 (m-30)
REVERT: B   41 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6894 (mt0)
REVERT: B  268 THR cc_start: 0.8424 (t) cc_final: 0.8175 (m)
REVERT: C   41 TYR cc_start: 0.6651 (p90) cc_final: 0.6112 (p90)
REVERT: C   76 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (p)
REVERT: D   93 ASP cc_start: 0.8190 (m-30) cc_final: 0.7718 (m-30)
  outliers start: 19
  outliers final: 12
  residues processed: 123
  average time/residue: 2.2258
  time to fit residues: 301.7126
Evaluate side-chains
  121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 57 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0870
   chunk 98 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 266 ASN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.171490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124632 restraints weight = 35181.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.07
r_work: 0.3234 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12071  Z= 0.105
  Angle     :  0.472   7.243  16405  Z= 0.251
  Chirality :  0.042   0.139   1783
  Planarity :  0.004   0.062   2158
  Dihedral  :  4.077  16.513   1651
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.16 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.22), residues: 1487
  helix:  2.58 (0.29), residues: 327
  sheet:  0.23 (0.24), residues: 443
  loop : -0.95 (0.22), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 426 
 TYR   0.011   0.001   TYR D  79 
 ARG   0.011   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03809 (  521)
  hydrogen bonds       : angle       4.35476 ( 1467)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       1.24307 (    2)
  covalent geometry    : bond        0.00243 (12068)
  covalent geometry    : angle       0.47186 (16403)
  Misc. bond           : bond        0.00364 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7250 (mp10) cc_final: 0.6337 (tm130)
REVERT: A  520 ASN cc_start: 0.8031 (t0) cc_final: 0.7560 (t0)
REVERT: A  614 ASP cc_start: 0.8313 (m-30) cc_final: 0.7986 (m-30)
REVERT: B   41 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6926 (mt0)
REVERT: B  268 THR cc_start: 0.8429 (t) cc_final: 0.8187 (m)
REVERT: B  346 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8200 (tt)
REVERT: C   41 TYR cc_start: 0.6649 (p90) cc_final: 0.6120 (p90)
REVERT: C   76 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7543 (p)
REVERT: D   93 ASP cc_start: 0.8210 (m-30) cc_final: 0.7743 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 121
  average time/residue: 2.2250
  time to fit residues: 297.6640
Evaluate side-chains
  123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.169677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123743 restraints weight = 35168.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.16
r_work: 0.3200 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12071  Z= 0.167
  Angle     :  0.517   7.768  16405  Z= 0.274
  Chirality :  0.043   0.147   1783
  Planarity :  0.004   0.062   2158
  Dihedral  :  4.203  16.732   1651
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.32 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.22), residues: 1487
  helix:  2.35 (0.28), residues: 330
  sheet:  0.16 (0.24), residues: 449
  loop : -1.02 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.017   0.001   PHE A 426 
 TYR   0.012   0.001   TYR D  79 
 ARG   0.013   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04393 (  521)
  hydrogen bonds       : angle       4.43504 ( 1467)
  SS BOND              : bond        0.00341 (    1)
  SS BOND              : angle       1.37545 (    2)
  covalent geometry    : bond        0.00408 (12068)
  covalent geometry    : angle       0.51662 (16403)
  Misc. bond           : bond        0.00379 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.936 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7276 (mp10) cc_final: 0.6353 (tm130)
REVERT: A  520 ASN cc_start: 0.8089 (t0) cc_final: 0.7639 (t0)
REVERT: A  614 ASP cc_start: 0.8324 (m-30) cc_final: 0.8065 (m-30)
REVERT: B   41 GLN cc_start: 0.7390 (tm-30) cc_final: 0.6948 (mt0)
REVERT: B  268 THR cc_start: 0.8494 (t) cc_final: 0.8248 (m)
REVERT: B  346 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: C   41 TYR cc_start: 0.6666 (p90) cc_final: 0.6279 (p90)
REVERT: C   76 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7629 (p)
REVERT: D   93 ASP cc_start: 0.8225 (m-30) cc_final: 0.7761 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 120
  average time/residue: 2.1261
  time to fit residues: 285.7781
Evaluate side-chains
  122 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.171268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.124725 restraints weight = 35454.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.13
r_work: 0.3203 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12071  Z= 0.157
  Angle     :  0.509   7.697  16405  Z= 0.271
  Chirality :  0.043   0.140   1783
  Planarity :  0.004   0.065   2158
  Dihedral  :  4.205  16.868   1651
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.72 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.22), residues: 1487
  helix:  2.32 (0.28), residues: 330
  sheet:  0.18 (0.24), residues: 449
  loop : -1.03 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 426 
 TYR   0.012   0.001   TYR D  79 
 ARG   0.013   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  521)
  hydrogen bonds       : angle       4.42827 ( 1467)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       1.34043 (    2)
  covalent geometry    : bond        0.00378 (12068)
  covalent geometry    : angle       0.50919 (16403)
  Misc. bond           : bond        0.00375 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7232 (mp10) cc_final: 0.6315 (tm130)
REVERT: A  520 ASN cc_start: 0.8041 (t0) cc_final: 0.7555 (t0)
REVERT: A  614 ASP cc_start: 0.8310 (m-30) cc_final: 0.8033 (m-30)
REVERT: B   41 GLN cc_start: 0.7384 (tm-30) cc_final: 0.6941 (mt0)
REVERT: B  268 THR cc_start: 0.8474 (t) cc_final: 0.8236 (m)
REVERT: B  346 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8163 (tt)
REVERT: C   41 TYR cc_start: 0.6638 (p90) cc_final: 0.6171 (p90)
REVERT: C   76 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7624 (p)
REVERT: D   93 ASP cc_start: 0.8097 (m-30) cc_final: 0.7639 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 117
  average time/residue: 2.1804
  time to fit residues: 282.4930
Evaluate side-chains
  120 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 119 optimal weight:    0.4980
   chunk 122 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 111 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.171439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125102 restraints weight = 35100.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.10
r_work: 0.3228 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12071  Z= 0.107
  Angle     :  0.472   7.756  16405  Z= 0.251
  Chirality :  0.042   0.138   1783
  Planarity :  0.004   0.069   2158
  Dihedral  :  4.052  16.347   1651
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.96 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.22), residues: 1487
  helix:  2.55 (0.29), residues: 331
  sheet:  0.28 (0.24), residues: 443
  loop : -0.95 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 348 
 HIS   0.005   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 426 
 TYR   0.011   0.001   TYR D  79 
 ARG   0.013   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  521)
  hydrogen bonds       : angle       4.31622 ( 1467)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       1.24898 (    2)
  covalent geometry    : bond        0.00249 (12068)
  covalent geometry    : angle       0.47208 (16403)
  Misc. bond           : bond        0.00363 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14239.60 seconds
wall clock time: 243 minutes 51.60 seconds (14631.60 seconds total)