Starting phenix.real_space_refine
on Fri Feb 14 21:09:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cny_45766/02_2025/9cny_45766.cif"
  }
  resolution = 4.0
  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=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    6562      2.51       5
     N    1770      2.21       5
     O    2048      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10410
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5042
          Classifications: {'peptide': 634}
          Link IDs: {'PTRANS': 25, 'TRANS': 608}
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 363
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 6, 'TRANS': 45}
    Chain: "D"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1732
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 11, 'TRANS': 202}
    Chain: "E"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 685
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
    Chain: "B"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2588
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 11, 'TRANS': 334}
          Chain breaks: 2
  Time building chain proxies: 5.93, per 1000 atoms: 0.57
  Number of scatterers: 10410
  At special positions: 0
  Unit cell: (102.153, 115.373, 139.409, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    2048      8.00
     N    1770      7.00
     C    6562      6.00
    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=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      24.5% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 3.831A  pdb=" N   ASP A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.696A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 361 through 367
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.554A  pdb=" N   LYS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 3.666A  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 542 through 553
      removed outlier: 3.504A  pdb=" N   TRP A 546 " --> pdb=" O   GLN A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 730
    Processing helix  chain 'A' and resid 750 through 754
      removed outlier: 3.710A  pdb=" N   GLN A 753 " --> pdb=" O   ASP A 750 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 44
      removed outlier: 4.409A  pdb=" N   TYR C  41 " --> pdb=" O   ASP C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
      removed outlier: 3.963A  pdb=" N   TYR C  65 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA C  66 " --> pdb=" O   GLY C  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 66'
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.568A  pdb=" N   ALA C  79 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.065A  pdb=" N   ALA D  57 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D  54 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN D  60 " --> pdb=" O   GLU D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 97
    Processing helix  chain 'D' and resid 104 through 118
    Processing helix  chain 'D' and resid 119 through 121
      No H-bonds generated for 'chain 'D' and resid 119 through 121'
    Processing helix  chain 'D' and resid 123 through 129
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.512A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.735A  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 241
      removed outlier: 3.686A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
      removed outlier: 3.586A  pdb=" N   SER E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183
      removed outlier: 6.428A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLN A 179 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276
      removed outlier: 7.300A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.110A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.110A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLN A 403 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 430
      removed outlier: 6.107A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 738 " --> pdb=" O   GLY A 771 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.846A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 6.541A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.724A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 3.926A  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 68
      removed outlier: 3.873A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118
      removed outlier: 6.459A  pdb=" N   GLY B 114 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR B 123 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR B 116 " --> pdb=" O   HIS B 121 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   HIS B 121 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.571A  pdb=" N   ALA B 173 " --> pdb=" O   TRP B 183 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.951A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.926A  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: 4.276A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.975A  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: 3.659A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 6.625A  pdb=" N   LEU B 346 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLN B 359 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   TRP B 348 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)

    467 hydrogen bonds defined for protein.
    1278 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: 3.77

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3479
        1.34 -     1.46: 2170
        1.46 -     1.58: 4938
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 10645
  Sorted by residual:
  bond pdb=" N   SER C  36 "
       pdb=" CA  SER C  36 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  bond pdb=" N   GLU E  24 "
       pdb=" CA  GLU E  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   ASP D  29 "
       pdb=" CA  ASP D  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N   VAL A 173 "
       pdb=" CA  VAL A 173 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.83e+00
  bond pdb=" N   VAL B  30 "
       pdb=" CA  VAL B  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.74e+00
  ... (remaining 10640 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 14150
        1.77 -     3.54: 263
        3.54 -     5.30: 65
        5.30 -     7.07: 1
        7.07 -     8.84: 1
  Bond angle restraints: 14480
  Sorted by residual:
  angle pdb=" CB  MET B 189 "
        pdb=" CG  MET B 189 "
        pdb=" SD  MET B 189 "
      ideal   model   delta    sigma   weight residual
     112.70  121.54   -8.84 3.00e+00 1.11e-01 8.68e+00
  angle pdb=" C   GLY A 184 "
        pdb=" N   ASN A 185 "
        pdb=" CA  ASN A 185 "
      ideal   model   delta    sigma   weight residual
     121.54  126.53   -4.99 1.91e+00 2.74e-01 6.83e+00
  angle pdb=" CA  LYS B  31 "
        pdb=" CB  LYS B  31 "
        pdb=" CG  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     114.10  119.05   -4.95 2.00e+00 2.50e-01 6.12e+00
  angle pdb=" N   VAL A 208 "
        pdb=" CA  VAL A 208 "
        pdb=" C   VAL A 208 "
      ideal   model   delta    sigma   weight residual
     113.71  111.40    2.31 9.50e-01 1.11e+00 5.93e+00
  angle pdb=" CA  ILE C  67 "
        pdb=" C   ILE C  67 "
        pdb=" N   PRO C  68 "
      ideal   model   delta    sigma   weight residual
     118.12  120.05   -1.93 8.10e-01 1.52e+00 5.65e+00
  ... (remaining 14475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5770
       17.98 -    35.96: 398
       35.96 -    53.94: 60
       53.94 -    71.93: 16
       71.93 -    89.91: 21
  Dihedral angle restraints: 6265
    sinusoidal: 2433
      harmonic: 3832
  Sorted by residual:
  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 -136.72   50.72     1      1.00e+01 1.00e-02 3.52e+01
  dihedral pdb=" CA  GLU B 127 "
           pdb=" C   GLU B 127 "
           pdb=" N   LYS B 128 "
           pdb=" CA  LYS B 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.62   24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ASN B 266 "
           pdb=" C   ASN B 266 "
           pdb=" N   LEU B 267 "
           pdb=" CA  LEU B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.66   23.34     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 996
       0.033 -    0.066: 381
       0.066 -    0.100: 110
       0.100 -    0.133: 74
       0.133 -    0.166: 8
  Chirality restraints: 1569
  Sorted by residual:
  chirality pdb=" CA  TRP A 546 "
            pdb=" N   TRP A 546 "
            pdb=" C   TRP A 546 "
            pdb=" CB  TRP A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.90e-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    2.58   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CB  THR D  53 "
            pdb=" CA  THR D  53 "
            pdb=" OG1 THR D  53 "
            pdb=" CG2 THR D  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1566 not shown)

  Planarity restraints: 1911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "    0.038 2.00e-02 2.50e+03   2.88e-02 2.07e+01
        pdb=" CG  TRP A 546 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 586 "   -0.042 5.00e-02 4.00e+02   6.25e-02 6.24e+00
        pdb=" N   PRO A 587 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 587 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 587 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 227 "   -0.181 9.50e-02 1.11e+02   8.14e-02 4.42e+00
        pdb=" NE  ARG A 227 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 227 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 227 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 227 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1908 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 113
        2.58 -     3.16: 9190
        3.16 -     3.74: 15953
        3.74 -     4.32: 21581
        4.32 -     4.90: 36260
  Nonbonded interactions: 83097
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 548 "
            pdb=" OG  SER A 551 "
     model   vdw
     2.003 3.040
  nonbonded pdb=" OG  SER A 715 "
            pdb=" OD1 ASP A 740 "
     model   vdw
     2.049 3.040
  nonbonded pdb=" OG1 THR A 423 "
            pdb=" OE1 GLN A 446 "
     model   vdw
     2.065 3.040
  nonbonded pdb=" OD1 ASP B 363 "
            pdb=" OH  TYR B 388 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OD1 ASP A 362 "
            pdb=" NH1 ARG A 366 "
     model   vdw
     2.133 3.120
  ... (remaining 83092 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.730
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10645  Z= 0.230
  Angle     :  0.629   8.838  14480  Z= 0.336
  Chirality :  0.044   0.166   1569
  Planarity :  0.005   0.081   1911
  Dihedral  : 13.796  89.908   3830
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.23), residues: 1319
  helix:  0.43 (0.30), residues: 269
  sheet:  0.21 (0.26), residues: 387
  loop : -0.08 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.078   0.002   TRP A 546 
 HIS   0.003   0.001   HIS B 165 
 PHE   0.028   0.002   PHE A 197 
 TYR   0.023   0.002   TYR D 205 
 ARG   0.010   0.001   ARG A 227 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7678 (mmt) cc_final: 0.7062 (mmt)
REVERT: A  489 LEU cc_start: 0.8514 (mm) cc_final: 0.8290 (mm)
REVERT: A  711 MET cc_start: 0.8933 (ppp) cc_final: 0.8542 (ttp)
REVERT: C   78 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8041 (mmtt)
REVERT: D  134 ASP cc_start: 0.8335 (p0) cc_final: 0.8109 (p0)
REVERT: D  183 GLU cc_start: 0.8152 (tp30) cc_final: 0.7917 (tp30)
REVERT: E   41 ASN cc_start: 0.8794 (t0) cc_final: 0.8427 (p0)
REVERT: B   82 LYS cc_start: 0.7664 (mtpt) cc_final: 0.6980 (mtmt)
REVERT: B  223 GLN cc_start: 0.8066 (tt0) cc_final: 0.7682 (tm-30)
REVERT: B  266 ASN cc_start: 0.7176 (m110) cc_final: 0.6674 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.2273
  time to fit residues: 71.6639
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0670
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 390 ASN
A 538 ASN
A 573 ASN
A 606 ASN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 GLN
B 334 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.143286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.112828 restraints weight = 19661.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111800 restraints weight = 17881.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112900 restraints weight = 17673.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10645  Z= 0.295
  Angle     :  0.652   8.044  14480  Z= 0.348
  Chirality :  0.047   0.191   1569
  Planarity :  0.004   0.043   1911
  Dihedral  :  5.184  26.376   1460
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.37 %
    Favored  : 88.56 %
  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:  0.04 (0.23), residues: 1319
  helix:  0.72 (0.31), residues: 279
  sheet:  0.00 (0.25), residues: 382
  loop : -0.14 (0.25), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.002   TRP A 546 
 HIS   0.009   0.001   HIS A 677 
 PHE   0.018   0.002   PHE A 197 
 TYR   0.021   0.002   TYR A 618 
 ARG   0.005   0.001   ARG A 583 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7934 (tp40) cc_final: 0.7220 (tm-30)
REVERT: A  369 MET cc_start: 0.7787 (mmt) cc_final: 0.7110 (mmt)
REVERT: A  483 VAL cc_start: 0.8821 (t) cc_final: 0.8392 (p)
REVERT: A  630 LEU cc_start: 0.9027 (tt) cc_final: 0.8726 (tp)
REVERT: A  711 MET cc_start: 0.8800 (ppp) cc_final: 0.7937 (ttp)
REVERT: A  768 MET cc_start: 0.6606 (mtm) cc_final: 0.6266 (ttm)
REVERT: A  777 MET cc_start: 0.9277 (tpp) cc_final: 0.8739 (tpt)
REVERT: C   39 GLU cc_start: 0.8406 (mp0) cc_final: 0.7867 (mp0)
REVERT: C   78 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7939 (mmtt)
REVERT: D   42 LYS cc_start: 0.8290 (tptm) cc_final: 0.8079 (tptt)
REVERT: D  134 ASP cc_start: 0.8564 (p0) cc_final: 0.8198 (p0)
REVERT: D  232 GLU cc_start: 0.8005 (tp30) cc_final: 0.7792 (tp30)
REVERT: E   53 GLN cc_start: 0.7829 (tp40) cc_final: 0.7573 (tp40)
REVERT: B   82 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7501 (mtmt)
REVERT: B  168 ASN cc_start: 0.8027 (p0) cc_final: 0.7648 (p0)
  outliers start: 23
  outliers final: 14
  residues processed: 193
  average time/residue: 0.2281
  time to fit residues: 62.1577
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  301 GLN
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 70 optimal weight:    0.0770
   chunk 84 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
E  52 GLN
E  96 ASN
B  64 HIS
** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.142933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111160 restraints weight = 20093.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110279 restraints weight = 16878.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111774 restraints weight = 17353.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10645  Z= 0.276
  Angle     :  0.613   7.116  14480  Z= 0.324
  Chirality :  0.045   0.175   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.959  26.256   1460
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.60 %
    Favored  : 83.87 %
  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: -0.02 (0.23), residues: 1319
  helix:  0.74 (0.31), residues: 281
  sheet: -0.06 (0.25), residues: 379
  loop : -0.20 (0.25), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 546 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.021   0.002   PHE A 197 
 TYR   0.017   0.002   TYR D 184 
 ARG   0.007   0.001   ARG A 391 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7877 (tp40) cc_final: 0.7160 (tm-30)
REVERT: A  287 LEU cc_start: 0.8425 (mm) cc_final: 0.8156 (tp)
REVERT: A  483 VAL cc_start: 0.8814 (t) cc_final: 0.8400 (p)
REVERT: A  617 THR cc_start: 0.9159 (m) cc_final: 0.8569 (p)
REVERT: A  646 MET cc_start: 0.7690 (tmm) cc_final: 0.7043 (tmm)
REVERT: A  711 MET cc_start: 0.8816 (ppp) cc_final: 0.7918 (ttp)
REVERT: C   39 GLU cc_start: 0.8454 (mp0) cc_final: 0.7963 (mp0)
REVERT: C   78 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7999 (mmtt)
REVERT: D  134 ASP cc_start: 0.8558 (p0) cc_final: 0.8268 (p0)
REVERT: D  136 ASP cc_start: 0.8365 (m-30) cc_final: 0.7965 (m-30)
REVERT: D  188 ARG cc_start: 0.8976 (tpp80) cc_final: 0.8493 (tpp80)
REVERT: D  207 ASP cc_start: 0.7837 (t70) cc_final: 0.7595 (t0)
REVERT: D  232 GLU cc_start: 0.7875 (tp30) cc_final: 0.7657 (tp30)
REVERT: E   53 GLN cc_start: 0.7900 (tp40) cc_final: 0.7671 (tp40)
REVERT: E   87 THR cc_start: 0.9019 (t) cc_final: 0.8759 (p)
REVERT: B  221 MET cc_start: 0.8542 (mpp) cc_final: 0.8189 (mpp)
REVERT: B  280 LYS cc_start: 0.8458 (ptmm) cc_final: 0.8078 (ptmm)
  outliers start: 28
  outliers final: 22
  residues processed: 194
  average time/residue: 0.2348
  time to fit residues: 64.6809
Evaluate side-chains
  184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 123 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 234 GLN
B 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.142289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.111194 restraints weight = 19715.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110552 restraints weight = 18114.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.111638 restraints weight = 17811.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10645  Z= 0.260
  Angle     :  0.593   6.968  14480  Z= 0.312
  Chirality :  0.044   0.167   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.807  26.037   1460
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.95 %
    Favored  : 81.44 %
  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:  0.03 (0.23), residues: 1319
  helix:  0.92 (0.32), residues: 275
  sheet: -0.08 (0.26), residues: 372
  loop : -0.19 (0.25), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 546 
 HIS   0.006   0.001   HIS A 677 
 PHE   0.021   0.002   PHE A 197 
 TYR   0.030   0.002   TYR A 609 
 ARG   0.007   0.000   ARG A 391 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7922 (tp40) cc_final: 0.7195 (tm-30)
REVERT: A  287 LEU cc_start: 0.8429 (mm) cc_final: 0.8180 (tp)
REVERT: A  412 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8913 (p)
REVERT: A  483 VAL cc_start: 0.8805 (t) cc_final: 0.8355 (p)
REVERT: A  617 THR cc_start: 0.9128 (m) cc_final: 0.8558 (p)
REVERT: A  677 HIS cc_start: 0.7221 (p-80) cc_final: 0.6353 (p90)
REVERT: A  711 MET cc_start: 0.8802 (ppp) cc_final: 0.8156 (ttp)
REVERT: A  768 MET cc_start: 0.6578 (mtm) cc_final: 0.6233 (ttm)
REVERT: C   39 GLU cc_start: 0.8520 (mp0) cc_final: 0.8078 (mp0)
REVERT: C   78 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7948 (mmtt)
REVERT: D  134 ASP cc_start: 0.8583 (p0) cc_final: 0.8103 (p0)
REVERT: D  136 ASP cc_start: 0.8444 (m-30) cc_final: 0.7955 (m-30)
REVERT: D  188 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8720 (tpp80)
REVERT: D  207 ASP cc_start: 0.7913 (t70) cc_final: 0.7709 (t0)
REVERT: E   87 THR cc_start: 0.9044 (t) cc_final: 0.8808 (p)
REVERT: B  221 MET cc_start: 0.8618 (mpp) cc_final: 0.8043 (mpp)
REVERT: B  223 GLN cc_start: 0.7245 (tp40) cc_final: 0.7017 (tp-100)
REVERT: B  280 LYS cc_start: 0.8576 (ptmm) cc_final: 0.8361 (ptmm)
  outliers start: 29
  outliers final: 24
  residues processed: 192
  average time/residue: 0.2386
  time to fit residues: 64.6621
Evaluate side-chains
  192 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 92 optimal weight:    0.3980
   chunk 78 optimal weight:    0.0980
   chunk 127 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0980
   chunk 73 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.143001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111004 restraints weight = 19760.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112270 restraints weight = 17501.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.112783 restraints weight = 15735.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10645  Z= 0.243
  Angle     :  0.586   7.191  14480  Z= 0.307
  Chirality :  0.043   0.210   1569
  Planarity :  0.004   0.044   1911
  Dihedral  :  4.711  25.561   1460
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.31 %
    Favored  : 80.45 %
  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: -0.01 (0.23), residues: 1319
  helix:  0.92 (0.32), residues: 275
  sheet: -0.20 (0.25), residues: 381
  loop : -0.16 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 317 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.021   0.001   PHE A 197 
 TYR   0.024   0.002   TYR A 609 
 ARG   0.007   0.000   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7931 (tp40) cc_final: 0.7196 (tm-30)
REVERT: A  287 LEU cc_start: 0.8396 (mm) cc_final: 0.8194 (tp)
REVERT: A  483 VAL cc_start: 0.8771 (t) cc_final: 0.8343 (p)
REVERT: A  617 THR cc_start: 0.9178 (m) cc_final: 0.8587 (p)
REVERT: A  711 MET cc_start: 0.8839 (ppp) cc_final: 0.8029 (ttp)
REVERT: A  768 MET cc_start: 0.6584 (mtm) cc_final: 0.6382 (ttm)
REVERT: C   39 GLU cc_start: 0.8648 (mp0) cc_final: 0.8117 (mp0)
REVERT: C   78 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8046 (mmtt)
REVERT: D  134 ASP cc_start: 0.8565 (p0) cc_final: 0.8281 (p0)
REVERT: D  188 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8673 (tpp80)
REVERT: D  207 ASP cc_start: 0.7869 (t70) cc_final: 0.7641 (t70)
REVERT: E   87 THR cc_start: 0.9032 (t) cc_final: 0.8779 (p)
REVERT: B  168 ASN cc_start: 0.8172 (p0) cc_final: 0.7810 (p0)
REVERT: B  221 MET cc_start: 0.8634 (mpp) cc_final: 0.7968 (mpp)
REVERT: B  223 GLN cc_start: 0.7193 (tp40) cc_final: 0.6894 (tp-100)
REVERT: B  231 ARG cc_start: 0.7506 (ttt180) cc_final: 0.7289 (ttt-90)
  outliers start: 36
  outliers final: 29
  residues processed: 194
  average time/residue: 0.2395
  time to fit residues: 65.1243
Evaluate side-chains
  194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 121 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0670
   chunk 9 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.7724

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.140875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.108773 restraints weight = 19893.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109524 restraints weight = 16401.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110440 restraints weight = 15580.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10645  Z= 0.349
  Angle     :  0.628   7.173  14480  Z= 0.333
  Chirality :  0.044   0.184   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.895  26.393   1460
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.48 %
    Favored  : 78.56 %
  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: -0.03 (0.23), residues: 1319
  helix:  0.85 (0.32), residues: 275
  sheet: -0.17 (0.25), residues: 385
  loop : -0.18 (0.25), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 546 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.019   0.002   PHE A 197 
 TYR   0.024   0.002   TYR A 609 
 ARG   0.006   0.001   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 166
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7937 (tp40) cc_final: 0.7214 (tm-30)
REVERT: A  287 LEU cc_start: 0.8421 (mm) cc_final: 0.8194 (tp)
REVERT: A  483 VAL cc_start: 0.8736 (t) cc_final: 0.8349 (p)
REVERT: A  586 PHE cc_start: 0.7535 (m-80) cc_final: 0.7199 (t80)
REVERT: A  617 THR cc_start: 0.9130 (m) cc_final: 0.8474 (p)
REVERT: A  646 MET cc_start: 0.7834 (tmm) cc_final: 0.7357 (tmm)
REVERT: A  711 MET cc_start: 0.8902 (ppp) cc_final: 0.8258 (ttp)
REVERT: A  768 MET cc_start: 0.6807 (mtm) cc_final: 0.6350 (ttm)
REVERT: C   39 GLU cc_start: 0.8728 (mp0) cc_final: 0.8418 (mp0)
REVERT: C   78 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8287 (mmtt)
REVERT: D  134 ASP cc_start: 0.8700 (p0) cc_final: 0.8328 (p0)
REVERT: D  188 ARG cc_start: 0.8976 (tpp80) cc_final: 0.8727 (tpp80)
REVERT: E   45 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8625 (ttpp)
REVERT: E   87 THR cc_start: 0.9050 (t) cc_final: 0.8828 (p)
REVERT: B  221 MET cc_start: 0.8594 (mpp) cc_final: 0.7895 (mpp)
REVERT: B  223 GLN cc_start: 0.7235 (tp40) cc_final: 0.6967 (tp-100)
REVERT: B  231 ARG cc_start: 0.7600 (ttt180) cc_final: 0.7337 (ttt-90)
  outliers start: 44
  outliers final: 35
  residues processed: 192
  average time/residue: 0.2328
  time to fit residues: 64.1420
Evaluate side-chains
  197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 SER
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   45 LYS
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0170
   chunk 81 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0970
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105456 restraints weight = 19938.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.104328 restraints weight = 20137.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105573 restraints weight = 17225.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10645  Z= 0.204
  Angle     :  0.593   8.444  14480  Z= 0.308
  Chirality :  0.043   0.162   1569
  Planarity :  0.004   0.044   1911
  Dihedral  :  4.641  24.973   1460
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.28 %
    Favored  : 77.84 %
  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:  0.06 (0.23), residues: 1319
  helix:  0.88 (0.32), residues: 277
  sheet: -0.11 (0.25), residues: 378
  loop : -0.11 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 317 
 HIS   0.002   0.001   HIS B 347 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.020   0.001   TYR A 585 
 ARG   0.007   0.000   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7935 (tp40) cc_final: 0.7234 (tm-30)
REVERT: A  325 MET cc_start: 0.8073 (mmm) cc_final: 0.7850 (mmp)
REVERT: A  483 VAL cc_start: 0.8718 (t) cc_final: 0.8250 (p)
REVERT: A  586 PHE cc_start: 0.7350 (m-80) cc_final: 0.6992 (t80)
REVERT: A  617 THR cc_start: 0.9173 (m) cc_final: 0.8578 (p)
REVERT: A  711 MET cc_start: 0.8840 (ppp) cc_final: 0.8246 (ttp)
REVERT: A  768 MET cc_start: 0.6707 (mtm) cc_final: 0.6365 (ttm)
REVERT: C   39 GLU cc_start: 0.8710 (mp0) cc_final: 0.8186 (mp0)
REVERT: C   49 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7567 (tp30)
REVERT: C   78 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8172 (mmtt)
REVERT: D  134 ASP cc_start: 0.8654 (p0) cc_final: 0.8178 (p0)
REVERT: D  188 ARG cc_start: 0.8900 (tpp80) cc_final: 0.8659 (tpp80)
REVERT: E   87 THR cc_start: 0.9035 (t) cc_final: 0.8801 (p)
REVERT: B  167 SER cc_start: 0.8767 (p) cc_final: 0.8499 (t)
REVERT: B  221 MET cc_start: 0.8540 (mpp) cc_final: 0.7783 (mpp)
REVERT: B  223 GLN cc_start: 0.7071 (tp40) cc_final: 0.6829 (tp-100)
  outliers start: 32
  outliers final: 27
  residues processed: 185
  average time/residue: 0.2350
  time to fit residues: 61.3228
Evaluate side-chains
  187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 121 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 119 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.104334 restraints weight = 19776.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.104508 restraints weight = 16490.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105681 restraints weight = 16444.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10645  Z= 0.216
  Angle     :  0.593   8.149  14480  Z= 0.307
  Chirality :  0.043   0.173   1569
  Planarity :  0.004   0.043   1911
  Dihedral  :  4.575  24.108   1460
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.01 %
    Favored  : 78.02 %
  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:  0.05 (0.23), residues: 1319
  helix:  0.87 (0.31), residues: 276
  sheet: -0.10 (0.25), residues: 375
  loop : -0.13 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.019   0.001   TYR A 585 
 ARG   0.008   0.000   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7962 (tp40) cc_final: 0.7299 (tm-30)
REVERT: A  287 LEU cc_start: 0.8111 (tp) cc_final: 0.7516 (tp)
REVERT: A  483 VAL cc_start: 0.8705 (t) cc_final: 0.8247 (p)
REVERT: A  586 PHE cc_start: 0.7348 (m-80) cc_final: 0.6965 (t80)
REVERT: A  617 THR cc_start: 0.9156 (m) cc_final: 0.8589 (p)
REVERT: A  711 MET cc_start: 0.8817 (ppp) cc_final: 0.8073 (ttp)
REVERT: A  768 MET cc_start: 0.6619 (mtm) cc_final: 0.6293 (ttm)
REVERT: C   39 GLU cc_start: 0.8786 (mp0) cc_final: 0.8471 (mp0)
REVERT: C   49 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7520 (tp30)
REVERT: D  134 ASP cc_start: 0.8687 (p0) cc_final: 0.8170 (p0)
REVERT: D  183 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7606 (tt0)
REVERT: D  188 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8623 (tpp80)
REVERT: E   87 THR cc_start: 0.9059 (t) cc_final: 0.8835 (p)
REVERT: B  167 SER cc_start: 0.8757 (p) cc_final: 0.8474 (t)
REVERT: B  221 MET cc_start: 0.8596 (mpp) cc_final: 0.7763 (mpp)
REVERT: B  316 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9094 (mp)
  outliers start: 33
  outliers final: 30
  residues processed: 179
  average time/residue: 0.2273
  time to fit residues: 57.9336
Evaluate side-chains
  190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0470
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9282

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

Flipped N/Q/H residues before XYZ refinement:
B 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.135867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102590 restraints weight = 19973.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.104201 restraints weight = 17885.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105743 restraints weight = 14059.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10645  Z= 0.222
  Angle     :  0.607   9.650  14480  Z= 0.313
  Chirality :  0.043   0.160   1569
  Planarity :  0.004   0.044   1911
  Dihedral  :  4.526  23.777   1460
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.64 %
    Favored  : 77.21 %
  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:  0.03 (0.23), residues: 1319
  helix:  0.84 (0.31), residues: 277
  sheet: -0.06 (0.25), residues: 374
  loop : -0.16 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.018   0.001   TYR A 585 
 ARG   0.007   0.000   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7939 (tp40) cc_final: 0.7276 (tm-30)
REVERT: A  287 LEU cc_start: 0.8071 (tp) cc_final: 0.7520 (tp)
REVERT: A  383 ASP cc_start: 0.7458 (m-30) cc_final: 0.7242 (m-30)
REVERT: A  483 VAL cc_start: 0.8709 (t) cc_final: 0.8242 (p)
REVERT: A  586 PHE cc_start: 0.7312 (m-80) cc_final: 0.6936 (t80)
REVERT: A  617 THR cc_start: 0.9160 (m) cc_final: 0.8587 (p)
REVERT: A  626 LYS cc_start: 0.8758 (mptt) cc_final: 0.8499 (mmtm)
REVERT: A  711 MET cc_start: 0.8814 (ppp) cc_final: 0.8058 (ttp)
REVERT: A  768 MET cc_start: 0.6794 (mtm) cc_final: 0.6430 (ttm)
REVERT: C   39 GLU cc_start: 0.8756 (mp0) cc_final: 0.8442 (mp0)
REVERT: C   49 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7507 (tp30)
REVERT: C   78 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7629 (mmtt)
REVERT: D  134 ASP cc_start: 0.8616 (p0) cc_final: 0.8390 (p0)
REVERT: D  183 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7623 (tt0)
REVERT: D  188 ARG cc_start: 0.8831 (tpp80) cc_final: 0.8590 (tpp80)
REVERT: E   50 MET cc_start: 0.7420 (tpp) cc_final: 0.6941 (tpp)
REVERT: E   87 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8835 (p)
REVERT: B  221 MET cc_start: 0.8650 (mpp) cc_final: 0.7678 (mpp)
REVERT: B  316 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9034 (mp)
  outliers start: 35
  outliers final: 29
  residues processed: 181
  average time/residue: 0.2359
  time to fit residues: 60.6861
Evaluate side-chains
  192 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.135658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102278 restraints weight = 19716.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103476 restraints weight = 18842.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.105009 restraints weight = 14795.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10645  Z= 0.217
  Angle     :  0.595   8.875  14480  Z= 0.307
  Chirality :  0.043   0.174   1569
  Planarity :  0.004   0.047   1911
  Dihedral  :  4.523  25.212   1460
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.82 %
    Favored  : 77.21 %
  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:  0.07 (0.23), residues: 1319
  helix:  0.89 (0.32), residues: 275
  sheet:  0.02 (0.25), residues: 383
  loop : -0.19 (0.25), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.017   0.001   TYR A 609 
 ARG   0.008   0.000   ARG A 321 

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7874 (tp40) cc_final: 0.7195 (tm-30)
REVERT: A  287 LEU cc_start: 0.8053 (tp) cc_final: 0.7387 (tp)
REVERT: A  383 ASP cc_start: 0.7496 (m-30) cc_final: 0.7293 (m-30)
REVERT: A  483 VAL cc_start: 0.8728 (t) cc_final: 0.8256 (p)
REVERT: A  586 PHE cc_start: 0.7316 (m-80) cc_final: 0.6938 (t80)
REVERT: A  617 THR cc_start: 0.9170 (m) cc_final: 0.8609 (p)
REVERT: A  626 LYS cc_start: 0.8792 (mptt) cc_final: 0.8509 (mmtm)
REVERT: A  711 MET cc_start: 0.8809 (ppp) cc_final: 0.8067 (ttp)
REVERT: A  768 MET cc_start: 0.6806 (mtm) cc_final: 0.6429 (ttm)
REVERT: C   39 GLU cc_start: 0.8765 (mp0) cc_final: 0.8417 (mp0)
REVERT: C   49 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7562 (tp30)
REVERT: C   78 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7703 (mmtt)
REVERT: D  134 ASP cc_start: 0.8609 (p0) cc_final: 0.8373 (p0)
REVERT: D  183 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7633 (tt0)
REVERT: D  188 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8594 (tpp80)
REVERT: E   87 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (p)
REVERT: B  221 MET cc_start: 0.8669 (mpp) cc_final: 0.7708 (mpp)
REVERT: B  316 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8983 (mp)
  outliers start: 33
  outliers final: 29
  residues processed: 186
  average time/residue: 0.2304
  time to fit residues: 60.2716
Evaluate side-chains
  194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 26 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.133020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.097066 restraints weight = 20249.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098975 restraints weight = 17462.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100748 restraints weight = 12681.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10645  Z= 0.313
  Angle     :  0.644   8.573  14480  Z= 0.337
  Chirality :  0.044   0.165   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.725  24.651   1460
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.82 %
    Favored  : 76.58 %
  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: -0.12 (0.23), residues: 1319
  helix:  0.70 (0.31), residues: 273
  sheet: -0.11 (0.25), residues: 380
  loop : -0.27 (0.25), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.023   0.002   PHE A 197 
 TYR   0.019   0.002   TYR A 609 
 ARG   0.007   0.001   ARG A 321 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2935.90 seconds
wall clock time: 53 minutes 37.54 seconds (3217.54 seconds total)