Starting phenix.real_space_refine
on Mon Jun  9 13:43:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cny_45766/06_2025/9cny_45766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cny_45766/06_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_45766/06_2025/9cny_45766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cny_45766/06_2025/9cny_45766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cny_45766/06_2025/9cny_45766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cny_45766/06_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-5710/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: 6.48, per 1000 atoms: 0.62
  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: 2.92
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.45
  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: 3.71

  Time building geometry restraints manager: 3.43 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.620
  Find NCS groups from input model:        0.110
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.500
-------------------------------------------------------------------------------
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  10646  Z= 0.156
  Angle     :  0.629   8.838  14482  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20612 (  463)
  hydrogen bonds       : angle       8.27080 ( 1278)
  SS BOND              : bond        0.00881 (    1)
  SS BOND              : angle       1.97544 (    2)
  covalent geometry    : bond        0.00348 (10645)
  covalent geometry    : angle       0.62909 (14480)

*********************** 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  : 1.313 
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: 0.2171
  time to fit residues: 69.1205
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  : 1.140 
-------------------------------------------------------------------------------
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 = 0.112829 restraints weight = 19661.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111800 restraints weight = 17881.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112900 restraints weight = 17672.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
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  10646  Z= 0.202
  Angle     :  0.652   8.044  14482  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04439 (  463)
  hydrogen bonds       : angle       5.79348 ( 1278)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.92038 (    2)
  covalent geometry    : bond        0.00450 (10645)
  covalent geometry    : angle       0.65195 (14480)

*********************** 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  : 1.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7934 (tp40) cc_final: 0.7221 (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: 0.6267 (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: 0.2423
  time to fit residues: 66.4944
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  : 1.245 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.1144

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.110709 restraints weight = 19984.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111105 restraints weight = 19365.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.112383 restraints weight = 16627.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10646  Z= 0.171
  Angle     :  0.602   7.250  14482  Z= 0.318
  Chirality :  0.045   0.176   1569
  Planarity :  0.004   0.044   1911
  Dihedral  :  4.913  25.905   1460
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.33 %
    Favored  : 84.41 %
  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:  0.78 (0.31), residues: 281
  sheet: -0.04 (0.25), residues: 380
  loop : -0.16 (0.25), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 546 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.020   0.002   PHE A 197 
 TYR   0.017   0.002   TYR D 184 
 ARG   0.008   0.001   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  463)
  hydrogen bonds       : angle       5.40292 ( 1278)
  SS BOND              : bond        0.00679 (    1)
  SS BOND              : angle       0.92226 (    2)
  covalent geometry    : bond        0.00380 (10645)
  covalent geometry    : angle       0.60200 (14480)

*********************** 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
  204 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7888 (tp40) cc_final: 0.7166 (tm-30)
REVERT: A  287 LEU cc_start: 0.8419 (mm) cc_final: 0.8160 (tp)
REVERT: A  483 VAL cc_start: 0.8772 (t) cc_final: 0.8365 (p)
REVERT: A  617 THR cc_start: 0.9171 (m) cc_final: 0.8575 (p)
REVERT: A  646 MET cc_start: 0.7717 (tmm) cc_final: 0.7034 (tmm)
REVERT: A  711 MET cc_start: 0.8838 (ppp) cc_final: 0.7956 (ttp)
REVERT: C   39 GLU cc_start: 0.8428 (mp0) cc_final: 0.7988 (mp0)
REVERT: C   78 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7980 (mmtt)
REVERT: D  134 ASP cc_start: 0.8541 (p0) cc_final: 0.8232 (p0)
REVERT: D  136 ASP cc_start: 0.8333 (m-30) cc_final: 0.7929 (m-30)
REVERT: D  187 GLU cc_start: 0.7888 (tt0) cc_final: 0.7381 (tm-30)
REVERT: D  188 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8352 (tpp80)
REVERT: D  207 ASP cc_start: 0.7783 (t70) cc_final: 0.7522 (t0)
REVERT: D  232 GLU cc_start: 0.7906 (tp30) cc_final: 0.7684 (tp30)
REVERT: E   53 GLN cc_start: 0.7868 (tp40) cc_final: 0.7649 (tp40)
REVERT: E   87 THR cc_start: 0.9000 (t) cc_final: 0.8706 (p)
REVERT: B  221 MET cc_start: 0.8569 (mpp) cc_final: 0.8215 (mpp)
REVERT: B  280 LYS cc_start: 0.8566 (ptmm) cc_final: 0.8220 (ptmm)
  outliers start: 25
  outliers final: 19
  residues processed: 192
  average time/residue: 0.2331
  time to fit residues: 64.3584
Evaluate side-chains
  183 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 446 GLN
B 234 GLN
B 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.144404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.113573 restraints weight = 19708.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113310 restraints weight = 17368.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.114412 restraints weight = 16819.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10646  Z= 0.134
  Angle     :  0.568   6.887  14482  Z= 0.298
  Chirality :  0.043   0.171   1569
  Planarity :  0.004   0.042   1911
  Dihedral  :  4.653  25.004   1460
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.05 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.23), residues: 1319
  helix:  1.00 (0.32), residues: 275
  sheet: -0.02 (0.25), residues: 374
  loop : -0.06 (0.25), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 546 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.019   0.001   PHE A 197 
 TYR   0.024   0.001   TYR A 609 
 ARG   0.006   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  463)
  hydrogen bonds       : angle       5.07159 ( 1278)
  SS BOND              : bond        0.00448 (    1)
  SS BOND              : angle       0.75695 (    2)
  covalent geometry    : bond        0.00303 (10645)
  covalent geometry    : angle       0.56757 (14480)

*********************** 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
  213 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 183
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7933 (tp40) cc_final: 0.7231 (tm-30)
REVERT: A  287 LEU cc_start: 0.8452 (mm) cc_final: 0.8251 (tp)
REVERT: A  412 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8898 (p)
REVERT: A  483 VAL cc_start: 0.8742 (t) cc_final: 0.8306 (p)
REVERT: A  617 THR cc_start: 0.9120 (m) cc_final: 0.8565 (p)
REVERT: A  677 HIS cc_start: 0.7268 (p-80) cc_final: 0.6352 (p90)
REVERT: A  711 MET cc_start: 0.8802 (ppp) cc_final: 0.8039 (ttp)
REVERT: A  768 MET cc_start: 0.6574 (mtm) cc_final: 0.6268 (ttm)
REVERT: C   39 GLU cc_start: 0.8535 (mp0) cc_final: 0.8072 (mp0)
REVERT: C   78 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7905 (mmtt)
REVERT: D  134 ASP cc_start: 0.8572 (p0) cc_final: 0.8261 (p0)
REVERT: D  188 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8683 (tpp80)
REVERT: D  207 ASP cc_start: 0.7983 (t70) cc_final: 0.7566 (t0)
REVERT: D  232 GLU cc_start: 0.7903 (tp30) cc_final: 0.7683 (tp30)
REVERT: E   87 THR cc_start: 0.9039 (t) cc_final: 0.8765 (p)
REVERT: B  168 ASN cc_start: 0.8108 (p0) cc_final: 0.7580 (p0)
REVERT: B  221 MET cc_start: 0.8644 (mpp) cc_final: 0.8029 (mpp)
REVERT: B  223 GLN cc_start: 0.7222 (tp40) cc_final: 0.7005 (tp-100)
REVERT: B  246 ASP cc_start: 0.8387 (p0) cc_final: 0.8005 (p0)
REVERT: B  280 LYS cc_start: 0.8653 (ptmm) cc_final: 0.8434 (ptmm)
  outliers start: 30
  outliers final: 24
  residues processed: 195
  average time/residue: 0.2312
  time to fit residues: 63.5865
Evaluate side-chains
  193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
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  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   68 SER
Chi-restraints excluded: chain D residue   73 LEU
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:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 127 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
E  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.132066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.093470 restraints weight = 20143.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.096347 restraints weight = 14026.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.098039 restraints weight = 11095.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10646  Z= 0.282
  Angle     :  0.660  10.109  14482  Z= 0.349
  Chirality :  0.045   0.245   1569
  Planarity :  0.004   0.048   1911
  Dihedral  :  4.944  26.689   1460
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.85 %
    Favored  : 79.46 %
  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:  0.84 (0.32), residues: 275
  sheet: -0.15 (0.25), residues: 382
  loop : -0.25 (0.25), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 635 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.020   0.002   PHE A 197 
 TYR   0.020   0.002   TYR A 609 
 ARG   0.005   0.001   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  463)
  hydrogen bonds       : angle       5.33369 ( 1278)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       8.12597 (    2)
  covalent geometry    : bond        0.00630 (10645)
  covalent geometry    : angle       0.65271 (14480)

*********************** 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
  206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 165
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.8021 (tp40) cc_final: 0.7284 (tm-30)
REVERT: A  287 LEU cc_start: 0.8476 (mm) cc_final: 0.8224 (tp)
REVERT: A  483 VAL cc_start: 0.8718 (t) cc_final: 0.8294 (p)
REVERT: A  617 THR cc_start: 0.9107 (m) cc_final: 0.8455 (p)
REVERT: A  711 MET cc_start: 0.9006 (ppp) cc_final: 0.8211 (ttp)
REVERT: A  768 MET cc_start: 0.6860 (mtm) cc_final: 0.6230 (ttm)
REVERT: C   39 GLU cc_start: 0.8768 (mp0) cc_final: 0.8482 (mp0)
REVERT: C   78 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8202 (mmtt)
REVERT: D  134 ASP cc_start: 0.8771 (p0) cc_final: 0.8448 (p0)
REVERT: D  207 ASP cc_start: 0.7876 (t70) cc_final: 0.7632 (t0)
REVERT: D  232 GLU cc_start: 0.8097 (tp30) cc_final: 0.7839 (tp30)
REVERT: E   87 THR cc_start: 0.9050 (t) cc_final: 0.8825 (p)
REVERT: B  221 MET cc_start: 0.8716 (mpp) cc_final: 0.8011 (mpp)
REVERT: B  223 GLN cc_start: 0.7515 (tp40) cc_final: 0.7205 (tp-100)
  outliers start: 41
  outliers final: 31
  residues processed: 188
  average time/residue: 0.2202
  time to fit residues: 59.9361
Evaluate side-chains
  189 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
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  514 THR
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  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:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 121 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.133074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.096289 restraints weight = 20229.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.099138 restraints weight = 12866.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.100161 restraints weight = 10280.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10646  Z= 0.210
  Angle     :  0.620   8.356  14482  Z= 0.325
  Chirality :  0.044   0.187   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.834  26.260   1460
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.39 %
    Favored  : 78.92 %
  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:  0.86 (0.32), residues: 275
  sheet: -0.22 (0.25), residues: 376
  loop : -0.19 (0.25), residues: 668

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   0.023   0.002   PHE A 197 
 TYR   0.023   0.002   TYR A 585 
 ARG   0.006   0.001   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  463)
  hydrogen bonds       : angle       5.20386 ( 1278)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       4.07691 (    2)
  covalent geometry    : bond        0.00472 (10645)
  covalent geometry    : angle       0.61803 (14480)

*********************** 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
  201 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 160
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.8028 (tp40) cc_final: 0.7305 (tm-30)
REVERT: A  287 LEU cc_start: 0.8460 (mm) cc_final: 0.8233 (tp)
REVERT: A  483 VAL cc_start: 0.8684 (t) cc_final: 0.8245 (p)
REVERT: A  617 THR cc_start: 0.9097 (m) cc_final: 0.8434 (p)
REVERT: A  711 MET cc_start: 0.8968 (ppp) cc_final: 0.8232 (ttp)
REVERT: A  768 MET cc_start: 0.6948 (mtm) cc_final: 0.6269 (ttm)
REVERT: C   39 GLU cc_start: 0.8832 (mp0) cc_final: 0.8486 (mp0)
REVERT: C   78 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8211 (mmtt)
REVERT: D  134 ASP cc_start: 0.8736 (p0) cc_final: 0.8371 (p0)
REVERT: D  232 GLU cc_start: 0.8036 (tp30) cc_final: 0.7791 (tp30)
REVERT: E   87 THR cc_start: 0.9008 (t) cc_final: 0.8757 (p)
REVERT: B  167 SER cc_start: 0.8866 (p) cc_final: 0.8615 (t)
REVERT: B  221 MET cc_start: 0.8721 (mpp) cc_final: 0.7913 (mpp)
REVERT: B  223 GLN cc_start: 0.7570 (tp40) cc_final: 0.7251 (tp-100)
  outliers start: 41
  outliers final: 31
  residues processed: 185
  average time/residue: 0.2283
  time to fit residues: 60.5029
Evaluate side-chains
  188 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
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  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  564 SER
Chi-restraints excluded: chain A residue  586 PHE
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  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   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  306 MET
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:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.100528 restraints weight = 20168.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102471 restraints weight = 18593.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.103552 restraints weight = 13473.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10646  Z= 0.191
  Angle     :  0.628   8.752  14482  Z= 0.325
  Chirality :  0.044   0.185   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.763  25.946   1460
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.83 %
    Favored  : 77.66 %
  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:  0.86 (0.31), residues: 275
  sheet: -0.20 (0.25), residues: 375
  loop : -0.19 (0.25), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 317 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.020   0.002   TYR A 585 
 ARG   0.007   0.001   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  463)
  hydrogen bonds       : angle       5.10240 ( 1278)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       6.66962 (    2)
  covalent geometry    : bond        0.00430 (10645)
  covalent geometry    : angle       0.62269 (14480)

*********************** 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
  207 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7992 (tp40) cc_final: 0.7292 (tm-30)
REVERT: A  287 LEU cc_start: 0.8428 (mm) cc_final: 0.8202 (tp)
REVERT: A  325 MET cc_start: 0.8056 (mmm) cc_final: 0.7806 (mmp)
REVERT: A  483 VAL cc_start: 0.8668 (t) cc_final: 0.8227 (p)
REVERT: A  586 PHE cc_start: 0.7653 (m-80) cc_final: 0.7160 (t80)
REVERT: A  617 THR cc_start: 0.9106 (m) cc_final: 0.8464 (p)
REVERT: A  650 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: A  711 MET cc_start: 0.8934 (ppp) cc_final: 0.8201 (ttp)
REVERT: A  768 MET cc_start: 0.6814 (mtm) cc_final: 0.6354 (ttm)
REVERT: C   39 GLU cc_start: 0.8821 (mp0) cc_final: 0.8469 (mp0)
REVERT: C   49 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7698 (tp30)
REVERT: D  134 ASP cc_start: 0.8795 (p0) cc_final: 0.8354 (p0)
REVERT: E   45 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8684 (ttpp)
REVERT: E   87 THR cc_start: 0.8975 (t) cc_final: 0.8733 (p)
REVERT: B  167 SER cc_start: 0.8852 (p) cc_final: 0.8601 (t)
REVERT: B  221 MET cc_start: 0.8656 (mpp) cc_final: 0.7856 (mpp)
REVERT: B  223 GLN cc_start: 0.7378 (tp40) cc_final: 0.7089 (tp-100)
  outliers start: 39
  outliers final: 34
  residues processed: 192
  average time/residue: 0.2250
  time to fit residues: 62.3933
Evaluate side-chains
  191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
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  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  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  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   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  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:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.136038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.102668 restraints weight = 20136.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102298 restraints weight = 12820.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103583 restraints weight = 11987.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10646  Z= 0.146
  Angle     :  0.609   8.255  14482  Z= 0.313
  Chirality :  0.043   0.169   1569
  Planarity :  0.004   0.042   1911
  Dihedral  :  4.615  24.966   1460
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.46 %
    Favored  : 77.48 %
  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:  0.92 (0.32), residues: 276
  sheet: -0.14 (0.25), residues: 381
  loop : -0.11 (0.26), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 677 
 PHE   0.023   0.001   PHE A 197 
 TYR   0.019   0.001   TYR A 585 
 ARG   0.008   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03295 (  463)
  hydrogen bonds       : angle       4.96141 ( 1278)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       5.26063 (    2)
  covalent geometry    : bond        0.00330 (10645)
  covalent geometry    : angle       0.60596 (14480)

*********************** 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
  197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.8037 (tp40) cc_final: 0.7317 (tm-30)
REVERT: A  483 VAL cc_start: 0.8670 (t) cc_final: 0.8206 (p)
REVERT: A  586 PHE cc_start: 0.7659 (m-80) cc_final: 0.7183 (t80)
REVERT: A  617 THR cc_start: 0.9154 (m) cc_final: 0.8547 (p)
REVERT: A  626 LYS cc_start: 0.8735 (mptt) cc_final: 0.8381 (mmtm)
REVERT: A  711 MET cc_start: 0.8919 (ppp) cc_final: 0.8226 (ttp)
REVERT: A  768 MET cc_start: 0.6774 (mtm) cc_final: 0.6317 (ttm)
REVERT: C   39 GLU cc_start: 0.8856 (mp0) cc_final: 0.8423 (mp0)
REVERT: C   78 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7786 (mmtt)
REVERT: D  134 ASP cc_start: 0.8748 (p0) cc_final: 0.8343 (p0)
REVERT: E   87 THR cc_start: 0.9003 (t) cc_final: 0.8753 (p)
REVERT: B  167 SER cc_start: 0.8800 (p) cc_final: 0.8538 (t)
REVERT: B  221 MET cc_start: 0.8716 (mpp) cc_final: 0.7807 (mpp)
REVERT: B  223 GLN cc_start: 0.7508 (tp40) cc_final: 0.7271 (tp-100)
  outliers start: 34
  outliers final: 31
  residues processed: 184
  average time/residue: 0.2199
  time to fit residues: 58.0226
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
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  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  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  564 SER
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  157 SER
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 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  306 MET
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:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 113 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0170
   chunk 71 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.4018

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.138173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105468 restraints weight = 20038.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107961 restraints weight = 17269.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108975 restraints weight = 12974.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10646  Z= 0.112
  Angle     :  0.603   9.552  14482  Z= 0.306
  Chirality :  0.043   0.158   1569
  Planarity :  0.004   0.041   1911
  Dihedral  :  4.452  22.982   1460
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.09 %
    Favored  : 77.30 %
  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:  0.15 (0.23), residues: 1319
  helix:  0.94 (0.32), residues: 277
  sheet:  0.04 (0.25), residues: 374
  loop : -0.11 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.020   0.001   PHE A 197 
 TYR   0.018   0.001   TYR A 585 
 ARG   0.008   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (  463)
  hydrogen bonds       : angle       4.81900 ( 1278)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       3.98760 (    2)
  covalent geometry    : bond        0.00254 (10645)
  covalent geometry    : angle       0.60117 (14480)

*********************** 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
  204 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7875 (tp40) cc_final: 0.7239 (tm-30)
REVERT: A  287 LEU cc_start: 0.7960 (tp) cc_final: 0.7449 (tp)
REVERT: A  483 VAL cc_start: 0.8648 (t) cc_final: 0.8179 (p)
REVERT: A  586 PHE cc_start: 0.7314 (m-80) cc_final: 0.6896 (t80)
REVERT: A  617 THR cc_start: 0.9131 (m) cc_final: 0.8583 (p)
REVERT: A  626 LYS cc_start: 0.8755 (mptt) cc_final: 0.8414 (mmtm)
REVERT: A  711 MET cc_start: 0.8796 (ppp) cc_final: 0.8217 (ttp)
REVERT: A  768 MET cc_start: 0.6660 (mtm) cc_final: 0.6243 (ttm)
REVERT: C   39 GLU cc_start: 0.8752 (mp0) cc_final: 0.8454 (mp0)
REVERT: C   78 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7669 (mmtt)
REVERT: D  183 GLU cc_start: 0.7880 (tp30) cc_final: 0.7616 (tt0)
REVERT: E   50 MET cc_start: 0.7403 (tpp) cc_final: 0.6898 (tpp)
REVERT: E   87 THR cc_start: 0.9038 (t) cc_final: 0.8784 (p)
REVERT: B  221 MET cc_start: 0.8691 (mpp) cc_final: 0.7767 (mpp)
REVERT: B  246 ASP cc_start: 0.8415 (p0) cc_final: 0.8178 (p0)
REVERT: B  316 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8934 (mp)
  outliers start: 29
  outliers final: 27
  residues processed: 190
  average time/residue: 0.2159
  time to fit residues: 58.7229
Evaluate side-chains
  197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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  668 ILE
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
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 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  306 MET
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:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 113 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.137718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107289 restraints weight = 19789.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106524 restraints weight = 17760.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107906 restraints weight = 16091.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10646  Z= 0.128
  Angle     :  0.606   8.864  14482  Z= 0.310
  Chirality :  0.043   0.158   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.418  22.348   1460
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.45 %
    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:  0.16 (0.23), residues: 1319
  helix:  0.95 (0.32), residues: 275
  sheet:  0.06 (0.25), residues: 379
  loop : -0.10 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.022   0.001   PHE A 197 
 TYR   0.033   0.001   TYR A 609 
 ARG   0.009   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (  463)
  hydrogen bonds       : angle       4.74862 ( 1278)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       3.41728 (    2)
  covalent geometry    : bond        0.00291 (10645)
  covalent geometry    : angle       0.60454 (14480)

********************** 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
  201 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7854 (tp40) cc_final: 0.7278 (tm-30)
REVERT: A  287 LEU cc_start: 0.8014 (tp) cc_final: 0.7493 (tp)
REVERT: A  483 VAL cc_start: 0.8736 (t) cc_final: 0.8264 (p)
REVERT: A  586 PHE cc_start: 0.7270 (m-80) cc_final: 0.6896 (t80)
REVERT: A  617 THR cc_start: 0.9142 (m) cc_final: 0.8606 (p)
REVERT: A  626 LYS cc_start: 0.8757 (mptt) cc_final: 0.8491 (mmtm)
REVERT: A  711 MET cc_start: 0.8779 (ppp) cc_final: 0.8518 (ttp)
REVERT: A  768 MET cc_start: 0.6604 (mtm) cc_final: 0.6288 (ttm)
REVERT: C   39 GLU cc_start: 0.8728 (mp0) cc_final: 0.8436 (mp0)
REVERT: C   78 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7574 (mmtt)
REVERT: D  183 GLU cc_start: 0.7815 (tp30) cc_final: 0.7597 (tt0)
REVERT: E   45 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8365 (ttpp)
REVERT: E   87 THR cc_start: 0.9098 (t) cc_final: 0.8883 (p)
REVERT: B  170 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6864 (mp10)
REVERT: B  221 MET cc_start: 0.8621 (mpp) cc_final: 0.7674 (mpp)
REVERT: B  316 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8979 (mp)
  outliers start: 33
  outliers final: 27
  residues processed: 186
  average time/residue: 0.2385
  time to fit residues: 64.0974
Evaluate side-chains
  194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
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  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  700 CYS
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 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   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  170 GLN
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 26 optimal weight:   20.0000
   chunk 46 optimal weight:    4.9990
   chunk 113 optimal weight:    0.0770
   chunk 7 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.5944

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

Flipped N/Q/H residues before XYZ refinement:
B 223 GLN
B 359 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.134367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.103376 restraints weight = 19863.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.102141 restraints weight = 16578.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.103351 restraints weight = 17951.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10646  Z= 0.215
  Angle     :  0.648   8.518  14482  Z= 0.337
  Chirality :  0.044   0.156   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.693  23.986   1460
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.18 %
    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: -0.05 (0.23), residues: 1319
  helix:  0.78 (0.32), residues: 276
  sheet: -0.09 (0.25), residues: 387
  loop : -0.24 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 317 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.024   0.002   PHE A 197 
 TYR   0.034   0.002   TYR A 609 
 ARG   0.008   0.001   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  463)
  hydrogen bonds       : angle       4.98258 ( 1278)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       3.01320 (    2)
  covalent geometry    : bond        0.00483 (10645)
  covalent geometry    : angle       0.64676 (14480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3364.22 seconds
wall clock time: 59 minutes 17.36 seconds (3557.36 seconds total)