Starting phenix.real_space_refine
on Tue Mar  3 17:20:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hc7_34654/03_2026/8hc7_34654.map"
  }
  resolution = 4.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4730      2.51       5
     N    1229      2.21       5
     O    1385      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7373
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3480
          Classifications: {'peptide': 430}
          Link IDs: {'PTRANS': 24, 'TRANS': 405}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2134
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 15, 'TRANS': 251}
    Chain: "H"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 868
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 2, 'TRANS': 112}
    Chain: "L"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 793
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.61, per 1000 atoms: 0.22
  Number of scatterers: 7373
  At special positions: 0
  Unit cell: (95.7, 105.6, 132, 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      29     16.00
     O    1385      8.00
     N    1229      7.00
     C    4730      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  15 " - pdb=" SG  CYS C 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
      " NAG C1301 " - " ASN C  61 "
      " NAG C1302 " - " ASN C 122 "
      " NAG C1303 " - " ASN C 165 "
      " NAG C1304 " - " ASN C 234 "
      " NAG C1305 " - " ASN C 282 "
      " NAG C1306 " - " ASN C 343 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 294.0 milliseconds
  

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 19 sheets defined
      6.7% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.838A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 389
      removed outlier: 3.895A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 410
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.388A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 342'
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.685A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.563A  pdb=" N   LEU A 390 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   CYS A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 386 through 391'
    Processing helix  chain 'A' and resid 406 through 411
      removed outlier: 3.849A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.513A  pdb=" N   ASN A 422 " --> pdb=" O   ILE A 418 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.620A  pdb=" N   ALA C  27 " --> pdb=" O   TRP C  64 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL C  62 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL C 267 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA C 264 " --> pdb=" O   ILE C  95 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C  91 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN C 188 " --> pdb=" O   GLU C  96 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU C 189 " --> pdb=" O   THR C 208 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR C 208 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.620A  pdb=" N   ALA C  27 " --> pdb=" O   TRP C  64 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL C  62 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL C 267 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA C 264 " --> pdb=" O   ILE C  95 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C  91 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN C 188 " --> pdb=" O   GLU C  96 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL C 193 " --> pdb=" O   TYR C 204 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS C 195 " --> pdb=" O   LYS C 202 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS C 202 " --> pdb=" O   LYS C 195 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE C 197 " --> pdb=" O   TYR C 200 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 51
      removed outlier: 4.039A  pdb=" N   HIS C  49 " --> pdb=" O   LEU C 277 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU C 277 " --> pdb=" O   HIS C  49 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR C  51 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   PHE C 275 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55
    Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85
    Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121
      removed outlier: 3.994A  pdb=" N   VAL C 120 " --> pdb=" O   VAL C 127 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL C 127 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 142
      removed outlier: 3.668A  pdb=" N   PHE C 140 " --> pdb=" O   ARG C 158 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ARG C 158 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU C 156 " --> pdb=" O   ASP C 142 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 356
      removed outlier: 3.836A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS C 356 " --> pdb=" O   ALA C 397 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ALA C 397 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR C 396 " --> pdb=" O   SER C 514 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER C 514 " --> pdb=" O   TYR C 396 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL C 512 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE C 400 " --> pdb=" O   VAL C 510 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 403
      removed outlier: 3.718A  pdb=" N   ASP A 398 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG A 509 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS A 432 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.652A  pdb=" N   ARG A 493 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.569A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 4.258A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN H  81 " --> pdb=" O   THR H  68 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11
      removed outlier: 7.098A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 113 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR H 110 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR H  93 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE H  92 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLY H  98 " --> pdb=" O   TYR H  33 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL H  50 " --> pdb=" O   PHE H  58 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 7.098A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 113 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR H 110 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR H  93 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LEU H  99 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LEU H 103 " --> pdb=" O   LEU H  99 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.683A  pdb=" N   GLU L 106 " --> pdb=" O   VAL L  11 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 46
      removed outlier: 3.792A  pdb=" N   GLN L  45 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN L  37 " --> pdb=" O   GLN L  45 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA L  34 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR L  36 " --> pdb=" O   TYR L  87 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR L  87 " --> pdb=" O   TYR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 48 through 49
      removed outlier: 3.877A  pdb=" N   TYR L  49 " --> pdb=" O   THR L  53 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR L  53 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'L' and resid 62 through 65
      removed outlier: 3.750A  pdb=" N   SER L  65 " --> pdb=" O   THR L  72 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR L  72 " --> pdb=" O   SER L  65 " (cutoff:3.500A)

    124 hydrogen bonds defined for protein.
    321 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2333
        1.34 -     1.46: 1956
        1.46 -     1.58: 3240
        1.58 -     1.70: 0
        1.70 -     1.82: 33
  Bond restraints: 7562
  Sorted by residual:
  bond pdb=" C1  NAG C1303 "
       pdb=" O5  NAG C1303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.86e+00
  bond pdb=" C1  NAG C1304 "
       pdb=" O5  NAG C1304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.58e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.52e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.52e+00
  bond pdb=" C1  NAG C1305 "
       pdb=" O5  NAG C1305 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.46e+00
  ... (remaining 7557 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 10084
        1.97 -     3.94: 163
        3.94 -     5.91: 27
        5.91 -     7.88: 2
        7.88 -     9.84: 2
  Bond angle restraints: 10278
  Sorted by residual:
  angle pdb=" CA  PHE C  79 "
        pdb=" CB  PHE C  79 "
        pdb=" CG  PHE C  79 "
      ideal   model   delta    sigma   weight residual
     113.80  116.84   -3.04 1.00e+00 1.00e+00 9.27e+00
  angle pdb=" C   PHE C  79 "
        pdb=" CA  PHE C  79 "
        pdb=" CB  PHE C  79 "
      ideal   model   delta    sigma   weight residual
     111.97  117.85   -5.88 1.99e+00 2.53e-01 8.74e+00
  angle pdb=" CB  GLN L  38 "
        pdb=" CG  GLN L  38 "
        pdb=" CD  GLN L  38 "
      ideal   model   delta    sigma   weight residual
     112.60  117.38   -4.78 1.70e+00 3.46e-01 7.92e+00
  angle pdb=" CA  LEU L  95 "
        pdb=" CB  LEU L  95 "
        pdb=" CG  LEU L  95 "
      ideal   model   delta    sigma   weight residual
     116.30  126.14   -9.84 3.50e+00 8.16e-02 7.91e+00
  angle pdb=" C   PHE A 374 "
        pdb=" N   PHE A 375 "
        pdb=" CA  PHE A 375 "
      ideal   model   delta    sigma   weight residual
     121.54  126.81   -5.27 1.91e+00 2.74e-01 7.62e+00
  ... (remaining 10273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 4046
       16.66 -    33.31: 387
       33.31 -    49.97: 90
       49.97 -    66.63: 11
       66.63 -    83.28: 10
  Dihedral angle restraints: 4544
    sinusoidal: 1874
      harmonic: 2670
  Sorted by residual:
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -152.66   66.66     1      1.00e+01 1.00e-02 5.80e+01
  dihedral pdb=" CB  CYS C  15 "
           pdb=" SG  CYS C  15 "
           pdb=" SG  CYS C 136 "
           pdb=" CB  CYS C 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.64   53.36     1      1.00e+01 1.00e-02 3.87e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.05   41.95     1      1.00e+01 1.00e-02 2.46e+01
  ... (remaining 4541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 697
       0.032 -    0.065: 283
       0.065 -    0.097: 102
       0.097 -    0.130: 51
       0.130 -    0.162: 7
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CB  ILE C  95 "
            pdb=" CA  ILE C  95 "
            pdb=" CG1 ILE C  95 "
            pdb=" CG2 ILE C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" C1  NAG C1302 "
            pdb=" ND2 ASN C 122 "
            pdb=" C2  NAG C1302 "
            pdb=" O5  NAG C1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" C1  NAG C1303 "
            pdb=" ND2 ASN C 165 "
            pdb=" C2  NAG C1303 "
            pdb=" O5  NAG C1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.36e-01
  ... (remaining 1137 not shown)

  Planarity restraints: 1324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.021 2.00e-02 2.50e+03   1.76e-02 7.73e+00
        pdb=" CG  TRP H  47 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  79 "   -0.014 2.00e-02 2.50e+03   2.09e-02 7.62e+00
        pdb=" CG  PHE C  79 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  79 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  79 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  79 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  79 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  79 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C  79 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.87e+00
        pdb=" C   PHE C  79 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   PHE C  79 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASP C  80 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1321 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1565
        2.78 -     3.31: 6064
        3.31 -     3.84: 11596
        3.84 -     4.37: 12460
        4.37 -     4.90: 21732
  Nonbonded interactions: 53417
  Sorted by model distance:
  nonbonded pdb=" O   ASP H  89 "
            pdb=" OH  TYR H  93 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   ASN A 360 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   LEU C  54 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG1 THR C 109 "
            pdb=" OD1 ASP C 111 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   PRO C  57 "
            pdb=" OG  SER C  60 "
     model   vdw
     2.370 3.040
  ... (remaining 53412 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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.240
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
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   0.040   7581  Z= 0.140
  Angle     :  0.609   9.844  10323  Z= 0.296
  Chirality :  0.045   0.162   1140
  Planarity :  0.004   0.033   1317
  Dihedral  : 13.294  83.284   2800
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.26), residues: 899
  helix: -3.58 (0.53), residues: 31
  sheet:  0.67 (0.42), residues: 168
  loop : -1.44 (0.21), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  24 
 TYR   0.014   0.001   TYR L  49 
 PHE   0.047   0.001   PHE C  79 
 TRP   0.048   0.001   TRP H  47 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7562)
  covalent geometry    : angle       0.60762 (10278)
  SS BOND              : bond        0.00170 (   12)
  SS BOND              : angle       0.52298 (   24)
  hydrogen bonds       : bond        0.31641 (  106)
  hydrogen bonds       : angle      11.57568 (  321)
  link_NAG-ASN         : bond        0.00335 (    7)
  link_NAG-ASN         : angle       1.22643 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   58 PHE cc_start: 0.7493 (m-10) cc_final: 0.6939 (m-10)
REVERT: H   84 SER cc_start: 0.7169 (p) cc_final: 0.6900 (p)
REVERT: L  104 LYS cc_start: 0.4952 (tptt) cc_final: 0.4743 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0896
  time to fit residues: 7.4408
Evaluate side-chains
  37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  49 HIS
C 481 ASN
A 360 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.107353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.086662 restraints weight = 36423.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.087512 restraints weight = 22459.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.088071 restraints weight = 16930.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.088051 restraints weight = 14899.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.088413 restraints weight = 13738.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7581  Z= 0.127
  Angle     :  0.515   6.489  10323  Z= 0.263
  Chirality :  0.042   0.165   1140
  Planarity :  0.003   0.035   1317
  Dihedral  :  4.310  34.959   1153
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.27), residues: 899
  helix: -3.24 (0.60), residues: 37
  sheet:  0.96 (0.41), residues: 183
  loop : -1.20 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.021   0.001   TYR H  52 
 PHE   0.012   0.001   PHE A 559 
 TRP   0.013   0.001   TRP C  64 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7562)
  covalent geometry    : angle       0.51160 (10278)
  SS BOND              : bond        0.00244 (   12)
  SS BOND              : angle       0.69995 (   24)
  hydrogen bonds       : bond        0.04756 (  106)
  hydrogen bonds       : angle       7.38257 (  321)
  link_NAG-ASN         : bond        0.00247 (    7)
  link_NAG-ASN         : angle       1.21674 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.282 
Fit side-chains
REVERT: C  223 LEU cc_start: 0.6989 (tp) cc_final: 0.6776 (tp)
REVERT: C  408 ARG cc_start: 0.8309 (tmm160) cc_final: 0.7968 (ptp-170)
REVERT: A  448 ASN cc_start: 0.7862 (t0) cc_final: 0.6969 (m-40)
REVERT: H   63 VAL cc_start: 0.7022 (m) cc_final: 0.6710 (m)
REVERT: L    3 GLN cc_start: 0.8729 (pp30) cc_final: 0.8290 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0943
  time to fit residues: 7.9358
Evaluate side-chains
  37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0970
   chunk 37 optimal weight:    0.4980
   chunk 79 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 185 ASN
L  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.103715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.083577 restraints weight = 34221.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.083510 restraints weight = 25085.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.084299 restraints weight = 20157.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.084280 restraints weight = 17870.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.084361 restraints weight = 16381.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7581  Z= 0.138
  Angle     :  0.527   8.515  10323  Z= 0.268
  Chirality :  0.042   0.172   1140
  Planarity :  0.003   0.026   1317
  Dihedral  :  4.124  30.643   1153
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.27), residues: 899
  helix: -3.22 (0.58), residues: 37
  sheet:  0.71 (0.41), residues: 173
  loop : -1.17 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  38 
 TYR   0.015   0.001   TYR H  93 
 PHE   0.015   0.001   PHE C  79 
 TRP   0.024   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7562)
  covalent geometry    : angle       0.52255 (10278)
  SS BOND              : bond        0.00348 (   12)
  SS BOND              : angle       1.01249 (   24)
  hydrogen bonds       : bond        0.04445 (  106)
  hydrogen bonds       : angle       7.02851 (  321)
  link_NAG-ASN         : bond        0.00311 (    7)
  link_NAG-ASN         : angle       1.28329 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: C  223 LEU cc_start: 0.7259 (tp) cc_final: 0.6950 (tp)
REVERT: C  408 ARG cc_start: 0.8331 (tmm160) cc_final: 0.7977 (ptp-170)
REVERT: L    3 GLN cc_start: 0.8747 (pp30) cc_final: 0.8289 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0866
  time to fit residues: 6.1603
Evaluate side-chains
  38 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
C  52 GLN
C 188 ASN
C 409 GLN
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
A 580 GLN
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
L  89 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.092822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.071749 restraints weight = 36571.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070963 restraints weight = 29564.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.071650 restraints weight = 28468.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.071826 restraints weight = 21841.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.072000 restraints weight = 20696.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106   7581  Z= 0.324
  Angle     :  0.829   9.268  10323  Z= 0.432
  Chirality :  0.049   0.236   1140
  Planarity :  0.006   0.042   1317
  Dihedral  :  6.762  51.943   1153
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 21.23
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.68 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.52 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.26), residues: 899
  helix: -3.59 (0.52), residues: 39
  sheet: -0.08 (0.40), residues: 177
  loop : -1.46 (0.22), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 457 
 TYR   0.030   0.003   TYR C 279 
 PHE   0.029   0.003   PHE C  43 
 TRP   0.014   0.002   TRP C  64 
 HIS   0.007   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 7562)
  covalent geometry    : angle       0.81977 (10278)
  SS BOND              : bond        0.00598 (   12)
  SS BOND              : angle       1.58892 (   24)
  hydrogen bonds       : bond        0.05040 (  106)
  hydrogen bonds       : angle       7.30146 (  321)
  link_NAG-ASN         : bond        0.00437 (    7)
  link_NAG-ASN         : angle       2.45863 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: C  223 LEU cc_start: 0.8278 (tp) cc_final: 0.7914 (tp)
REVERT: C  273 ARG cc_start: 0.3825 (ttt-90) cc_final: 0.3521 (ttt180)
REVERT: A  532 ASN cc_start: 0.8434 (m-40) cc_final: 0.8197 (p0)
REVERT: H   34 MET cc_start: 0.8158 (mmp) cc_final: 0.7904 (mmm)
REVERT: L    3 GLN cc_start: 0.8554 (pp30) cc_final: 0.8147 (pp30)
REVERT: L   89 GLN cc_start: 0.5319 (OUTLIER) cc_final: 0.4736 (tp-100)
  outliers start: 4
  outliers final: 2
  residues processed: 54
  average time/residue: 0.0754
  time to fit residues: 5.7945
Evaluate side-chains
  34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.0980
   chunk 73 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0010
   chunk 27 optimal weight:    5.9990
   chunk 23 optimal weight:    0.3980
   chunk 35 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.097006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075142 restraints weight = 35094.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.074268 restraints weight = 32081.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.074493 restraints weight = 27161.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.074907 restraints weight = 23800.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.075185 restraints weight = 21553.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7581  Z= 0.113
  Angle     :  0.569   7.944  10323  Z= 0.289
  Chirality :  0.044   0.160   1140
  Planarity :  0.003   0.037   1317
  Dihedral  :  5.360  52.846   1153
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.27), residues: 899
  helix: -3.02 (0.68), residues: 31
  sheet:  0.25 (0.40), residues: 192
  loop : -1.17 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.010   0.001   TYR A 396 
 PHE   0.010   0.001   PHE A 562 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7562)
  covalent geometry    : angle       0.56194 (10278)
  SS BOND              : bond        0.00394 (   12)
  SS BOND              : angle       0.92066 (   24)
  hydrogen bonds       : bond        0.03893 (  106)
  hydrogen bonds       : angle       6.80245 (  321)
  link_NAG-ASN         : bond        0.00691 (    7)
  link_NAG-ASN         : angle       1.96347 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  273 ARG cc_start: 0.4146 (ttt-90) cc_final: 0.3944 (ttt-90)
REVERT: H   34 MET cc_start: 0.7595 (mmp) cc_final: 0.7352 (mmm)
REVERT: L    3 GLN cc_start: 0.8613 (pp30) cc_final: 0.8212 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0988
  time to fit residues: 7.5289
Evaluate side-chains
  37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0770
   chunk 23 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.094404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073685 restraints weight = 33321.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.073561 restraints weight = 26732.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.074033 restraints weight = 25385.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.074360 restraints weight = 19298.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.074523 restraints weight = 17954.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   7581  Z= 0.211
  Angle     :  0.648  10.892  10323  Z= 0.327
  Chirality :  0.044   0.274   1140
  Planarity :  0.004   0.037   1317
  Dihedral  :  5.603  45.212   1153
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.27), residues: 899
  helix: -3.51 (0.48), residues: 46
  sheet:  0.30 (0.41), residues: 187
  loop : -1.45 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.020   0.002   TYR C 473 
 PHE   0.013   0.002   PHE A 562 
 TRP   0.026   0.002   TRP H 106 
 HIS   0.003   0.001   HIS C 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 7562)
  covalent geometry    : angle       0.64030 (10278)
  SS BOND              : bond        0.00514 (   12)
  SS BOND              : angle       1.18325 (   24)
  hydrogen bonds       : bond        0.04078 (  106)
  hydrogen bonds       : angle       6.59843 (  321)
  link_NAG-ASN         : bond        0.00299 (    7)
  link_NAG-ASN         : angle       1.99822 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: C   56 LEU cc_start: 0.9707 (tp) cc_final: 0.9473 (tt)
REVERT: C  223 LEU cc_start: 0.8165 (tp) cc_final: 0.7770 (tp)
REVERT: L    3 GLN cc_start: 0.8470 (pp30) cc_final: 0.7974 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0807
  time to fit residues: 5.7112
Evaluate side-chains
  30 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 83 optimal weight:    0.2980
   chunk 29 optimal weight:    6.9990
   chunk 59 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C  17 ASN
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.096479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.075743 restraints weight = 32872.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.075529 restraints weight = 25259.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.076208 restraints weight = 23140.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.076337 restraints weight = 18119.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.076468 restraints weight = 17461.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7581  Z= 0.105
  Angle     :  0.553   7.479  10323  Z= 0.278
  Chirality :  0.044   0.184   1140
  Planarity :  0.003   0.032   1317
  Dihedral  :  5.035  44.590   1153
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.27), residues: 899
  helix: -3.49 (0.53), residues: 39
  sheet:  0.37 (0.42), residues: 184
  loop : -1.40 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.008   0.001   TYR C  37 
 PHE   0.014   0.001   PHE A 565 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7562)
  covalent geometry    : angle       0.54797 (10278)
  SS BOND              : bond        0.00377 (   12)
  SS BOND              : angle       1.06062 (   24)
  hydrogen bonds       : bond        0.03463 (  106)
  hydrogen bonds       : angle       6.34780 (  321)
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       1.52544 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  223 LEU cc_start: 0.8070 (tp) cc_final: 0.7835 (tp)
REVERT: H   51 LEU cc_start: 0.9005 (tp) cc_final: 0.8798 (tp)
REVERT: L    3 GLN cc_start: 0.8345 (pp30) cc_final: 0.7943 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0932
  time to fit residues: 6.5213
Evaluate side-chains
  34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** 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 = 0.3871 r_free = 0.3871 target = 0.096401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.074999 restraints weight = 33651.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.074978 restraints weight = 23815.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.075588 restraints weight = 20647.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.075795 restraints weight = 18045.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.075968 restraints weight = 17249.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7581  Z= 0.110
  Angle     :  0.552   7.726  10323  Z= 0.277
  Chirality :  0.043   0.161   1140
  Planarity :  0.003   0.031   1317
  Dihedral  :  4.835  37.391   1153
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.27), residues: 899
  helix: -3.32 (0.56), residues: 39
  sheet:  0.42 (0.42), residues: 184
  loop : -1.42 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.020   0.001   TYR C 473 
 PHE   0.011   0.001   PHE C  79 
 TRP   0.028   0.002   TRP H  47 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7562)
  covalent geometry    : angle       0.54683 (10278)
  SS BOND              : bond        0.00382 (   12)
  SS BOND              : angle       0.92207 (   24)
  hydrogen bonds       : bond        0.03391 (  106)
  hydrogen bonds       : angle       6.24870 (  321)
  link_NAG-ASN         : bond        0.00251 (    7)
  link_NAG-ASN         : angle       1.51774 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  223 LEU cc_start: 0.8195 (tp) cc_final: 0.7915 (tp)
REVERT: H   34 MET cc_start: 0.8494 (mmm) cc_final: 0.7403 (mmm)
REVERT: L    3 GLN cc_start: 0.8420 (pp30) cc_final: 0.7983 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1002
  time to fit residues: 6.2408
Evaluate side-chains
  33 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 82 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.096693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.075656 restraints weight = 36192.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.075002 restraints weight = 28282.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.075722 restraints weight = 24504.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.075705 restraints weight = 21722.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.075917 restraints weight = 19596.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7581  Z= 0.108
  Angle     :  0.556   8.766  10323  Z= 0.279
  Chirality :  0.043   0.162   1140
  Planarity :  0.003   0.030   1317
  Dihedral  :  4.683  34.660   1153
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.27), residues: 899
  helix: -3.19 (0.50), residues: 51
  sheet:  0.51 (0.40), residues: 200
  loop : -1.49 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.008   0.001   TYR C 265 
 PHE   0.014   0.001   PHE C 374 
 TRP   0.027   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7562)
  covalent geometry    : angle       0.55155 (10278)
  SS BOND              : bond        0.00368 (   12)
  SS BOND              : angle       0.83703 (   24)
  hydrogen bonds       : bond        0.03307 (  106)
  hydrogen bonds       : angle       6.18829 (  321)
  link_NAG-ASN         : bond        0.00252 (    7)
  link_NAG-ASN         : angle       1.43759 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  223 LEU cc_start: 0.8160 (tp) cc_final: 0.7896 (tp)
REVERT: C  489 TYR cc_start: 0.6558 (p90) cc_final: 0.6280 (p90)
REVERT: L    3 GLN cc_start: 0.8472 (pp30) cc_final: 0.7972 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0944
  time to fit residues: 6.3383
Evaluate side-chains
  33 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0770
   chunk 58 optimal weight:    0.0070
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.097208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.075861 restraints weight = 36353.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.075874 restraints weight = 26995.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.076478 restraints weight = 21935.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.076307 restraints weight = 19952.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.076546 restraints weight = 18446.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7581  Z= 0.101
  Angle     :  0.558   8.562  10323  Z= 0.280
  Chirality :  0.043   0.163   1140
  Planarity :  0.003   0.065   1317
  Dihedral  :  4.586  32.621   1153
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.27), residues: 899
  helix: -3.21 (0.51), residues: 51
  sheet:  0.32 (0.39), residues: 215
  loop : -1.46 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 102 
 TYR   0.021   0.001   TYR C 473 
 PHE   0.013   0.001   PHE C  79 
 TRP   0.023   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7562)
  covalent geometry    : angle       0.55411 (10278)
  SS BOND              : bond        0.00340 (   12)
  SS BOND              : angle       0.90872 (   24)
  hydrogen bonds       : bond        0.03256 (  106)
  hydrogen bonds       : angle       6.13408 (  321)
  link_NAG-ASN         : bond        0.00323 (    7)
  link_NAG-ASN         : angle       1.38620 (   21)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  489 TYR cc_start: 0.6719 (p90) cc_final: 0.6353 (p90)
REVERT: H   34 MET cc_start: 0.8525 (mmm) cc_final: 0.7351 (mmm)
REVERT: L    4 MET cc_start: 0.5699 (mmp) cc_final: 0.4904 (mmp)
REVERT: L   24 ARG cc_start: 0.7152 (tpt-90) cc_final: 0.6656 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1052
  time to fit residues: 6.7417
Evaluate side-chains
  35 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 43 optimal weight:    0.2980
   chunk 86 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.091821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.072015 restraints weight = 36579.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.070888 restraints weight = 30872.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.071542 restraints weight = 31518.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.071691 restraints weight = 23675.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.071789 restraints weight = 23687.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.6368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   7581  Z= 0.253
  Angle     :  0.717   9.430  10323  Z= 0.366
  Chirality :  0.046   0.210   1140
  Planarity :  0.005   0.051   1317
  Dihedral  :  5.907  41.996   1153
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.01 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.27), residues: 899
  helix: -3.25 (0.54), residues: 45
  sheet: -0.06 (0.41), residues: 198
  loop : -1.55 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 457 
 TYR   0.017   0.002   TYR C 279 
 PHE   0.017   0.002   PHE A 565 
 TRP   0.022   0.002   TRP L  35 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 7562)
  covalent geometry    : angle       0.71073 (10278)
  SS BOND              : bond        0.00527 (   12)
  SS BOND              : angle       1.14903 (   24)
  hydrogen bonds       : bond        0.03994 (  106)
  hydrogen bonds       : angle       6.88756 (  321)
  link_NAG-ASN         : bond        0.00317 (    7)
  link_NAG-ASN         : angle       2.07625 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1135.01 seconds
wall clock time: 20 minutes 22.94 seconds (1222.94 seconds total)