Starting phenix.real_space_refine
on Tue Jul 29 14:39:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iux_35729/07_2025/8iux_35729.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.070
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      63      5.16       5
     C    7104      2.51       5
     N    2037      2.21       5
     O    2268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11472
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3782
          Classifications: {'peptide': 484}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 469}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 8.16, per 1000 atoms: 0.71
  Number of scatterers: 11472
  At special positions: 0
  Unit cell: (85.004, 85.004, 149.564, 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      63     16.00
     O    2268      8.00
     N    2037      7.00
     C    7104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   5 " - pdb=" SG  CYS A 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A 269 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 273 " - pdb=" SG  CYS A 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   5 " - pdb=" SG  CYS C 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   5 " - pdb=" SG  CYS B 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 269 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  43 " - pdb=" SG  CYS B 269 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  88 " - pdb=" SG  CYS C 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  88 " - pdb=" SG  CYS B 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 273 " - pdb=" SG  CYS C 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 297 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 470 " - pdb=" SG  CYS C 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 470 " - pdb=" SG  CYS B 474 " 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 501 " - " ASN A 408 "
      " NAG A 502 " - " ASN A  29 "
      " NAG A 503 " - " ASN A 480 "
      " NAG B 501 " - " ASN B 408 "
      " NAG B 502 " - " ASN B  29 "
      " NAG B 503 " - " ASN B 480 "
      " NAG C 501 " - " ASN C 408 "
      " NAG C 502 " - " ASN C  29 "
      " NAG C 503 " - " ASN C 480 "
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2640

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 30 sheets defined
      22.5% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 105
      removed outlier: 3.658A  pdb=" N   LEU A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU A 105 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 187
      removed outlier: 3.673A  pdb=" N   LYS A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 382
      removed outlier: 3.637A  pdb=" N   THR A 367 " --> pdb=" O   ASP A 363 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLN A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 376 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 377 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG A 380 " --> pdb=" O   GLY A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 452
      removed outlier: 3.613A  pdb=" N   VAL A 406 " --> pdb=" O   GLN A 402 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 416 " --> pdb=" O   ASP A 412 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 480
      removed outlier: 3.596A  pdb=" N   SER A 477 " --> pdb=" O   ASP A 473 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE A 478 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 479 " --> pdb=" O   MET A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 493
    Processing helix  chain 'B' and resid 95 through 105
      removed outlier: 3.657A  pdb=" N   LEU B  99 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU B 105 " --> pdb=" O   GLN B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 187
      removed outlier: 3.672A  pdb=" N   LYS B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 382
      removed outlier: 3.637A  pdb=" N   THR B 367 " --> pdb=" O   ASP B 363 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER B 369 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLN B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 376 " --> pdb=" O   ASP B 372 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B 377 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B 380 " --> pdb=" O   GLY B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 452
      removed outlier: 3.613A  pdb=" N   VAL B 406 " --> pdb=" O   GLN B 402 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU B 416 " --> pdb=" O   ASP B 412 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU B 423 " --> pdb=" O   SER B 419 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU B 440 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 480
      removed outlier: 3.596A  pdb=" N   SER B 477 " --> pdb=" O   ASP B 473 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 478 " --> pdb=" O   CYS B 474 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG B 479 " --> pdb=" O   MET B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 493
    Processing helix  chain 'C' and resid 95 through 105
      removed outlier: 3.658A  pdb=" N   LEU C  99 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE C 102 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLU C 105 " --> pdb=" O   GLN C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 187
      removed outlier: 3.673A  pdb=" N   LYS C 185 " --> pdb=" O   ALA C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 382
      removed outlier: 3.637A  pdb=" N   THR C 367 " --> pdb=" O   ASP C 363 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER C 369 " --> pdb=" O   LYS C 365 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLN C 373 " --> pdb=" O   SER C 369 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY C 376 " --> pdb=" O   ASP C 372 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS C 377 " --> pdb=" O   GLN C 373 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG C 380 " --> pdb=" O   GLY C 376 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 452
      removed outlier: 3.614A  pdb=" N   VAL C 406 " --> pdb=" O   GLN C 402 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU C 416 " --> pdb=" O   ASP C 412 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU C 423 " --> pdb=" O   SER C 419 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU C 440 " --> pdb=" O   LEU C 436 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   MET C 441 " --> pdb=" O   ALA C 437 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL C 448 " --> pdb=" O   LEU C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 480
      removed outlier: 3.597A  pdb=" N   SER C 477 " --> pdb=" O   ASP C 473 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE C 478 " --> pdb=" O   CYS C 474 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG C 479 " --> pdb=" O   MET C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 488 through 493
    Processing sheet with id=1, first strand: chain 'A' and resid 357 through 360
      removed outlier: 3.745A  pdb=" N   GLY A 359 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU A 457 " --> pdb=" O   GLU A 465 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 15 through 17
    Processing sheet with id=3, first strand: chain 'A' and resid 30 through 32
    Processing sheet with id=4, first strand: chain 'A' and resid 34 through 35
    Processing sheet with id=5, first strand: chain 'A' and resid 42 through 43
      removed outlier: 5.700A  pdb=" N   ILE A  42 " --> pdb=" O   ASP A 266 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=5
    Processing sheet with id=6, first strand: chain 'A' and resid 49 through 51
      removed outlier: 6.076A  pdb=" N   ILE A  78 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'A' and resid 91 through 93
      removed outlier: 7.002A  pdb=" N   LYS A  92 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   TRP A 226 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   VAL A 171 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE A 243 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 144 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'A' and resid 110 through 113
      removed outlier: 3.544A  pdb=" N   GLU A 112 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'A' and resid 156 through 161
    Processing sheet with id=10, first strand: chain 'A' and resid 278 through 279
      removed outlier: 3.534A  pdb=" N   GLY A 278 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'B' and resid 357 through 360
      removed outlier: 3.745A  pdb=" N   GLY B 359 " --> pdb=" O   HIS B 352 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU B 457 " --> pdb=" O   GLU B 465 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'B' and resid 15 through 17
    Processing sheet with id=13, first strand: chain 'B' and resid 30 through 32
    Processing sheet with id=14, first strand: chain 'B' and resid 34 through 35
    Processing sheet with id=15, first strand: chain 'B' and resid 42 through 43
      removed outlier: 5.700A  pdb=" N   ILE B  42 " --> pdb=" O   ASP B 266 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=15
    Processing sheet with id=16, first strand: chain 'B' and resid 49 through 51
      removed outlier: 6.076A  pdb=" N   ILE B  78 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'B' and resid 91 through 93
      removed outlier: 7.001A  pdb=" N   LYS B  92 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   TRP B 226 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   VAL B 171 " --> pdb=" O   PRO B 246 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE B 243 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 144 " --> pdb=" O   PHE B 243 " (cutoff:3.500A)
    Processing sheet with id=18, first strand: chain 'B' and resid 110 through 113
      removed outlier: 3.544A  pdb=" N   GLU B 112 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'B' and resid 156 through 161
    Processing sheet with id=20, first strand: chain 'B' and resid 278 through 279
      removed outlier: 3.534A  pdb=" N   GLY B 278 " --> pdb=" O   HIS B 275 " (cutoff:3.500A)
    Processing sheet with id=21, first strand: chain 'C' and resid 357 through 360
      removed outlier: 3.745A  pdb=" N   GLY C 359 " --> pdb=" O   HIS C 352 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU C 457 " --> pdb=" O   GLU C 465 " (cutoff:3.500A)
    Processing sheet with id=22, first strand: chain 'C' and resid 15 through 17
    Processing sheet with id=23, first strand: chain 'C' and resid 30 through 32
    Processing sheet with id=24, first strand: chain 'C' and resid 34 through 35
    Processing sheet with id=25, first strand: chain 'C' and resid 42 through 43
      removed outlier: 5.700A  pdb=" N   ILE C  42 " --> pdb=" O   ASP C 266 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=25
    Processing sheet with id=26, first strand: chain 'C' and resid 49 through 51
      removed outlier: 6.075A  pdb=" N   ILE C  78 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing sheet with id=27, first strand: chain 'C' and resid 91 through 93
      removed outlier: 7.001A  pdb=" N   LYS C  92 " --> pdb=" O   PHE C 224 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   TRP C 226 " --> pdb=" O   LYS C  92 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   VAL C 171 " --> pdb=" O   PRO C 246 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE C 243 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU C 144 " --> pdb=" O   PHE C 243 " (cutoff:3.500A)
    Processing sheet with id=28, first strand: chain 'C' and resid 110 through 113
      removed outlier: 3.544A  pdb=" N   GLU C 112 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
    Processing sheet with id=29, first strand: chain 'C' and resid 156 through 161
    Processing sheet with id=30, first strand: chain 'C' and resid 278 through 279
      removed outlier: 3.534A  pdb=" N   GLY C 278 " --> pdb=" O   HIS C 275 " (cutoff:3.500A)

    354 hydrogen bonds defined for protein.
    981 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.41

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3904
        1.34 -     1.46: 2648
        1.46 -     1.58: 5040
        1.58 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 11682
  Sorted by residual:
  bond pdb=" C1  NAG A 503 "
       pdb=" O5  NAG A 503 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C1  NAG C 503 "
       pdb=" O5  NAG C 503 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.17e+00
  bond pdb=" C1  NAG B 503 "
       pdb=" O5  NAG B 503 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" CA  GLY B  53 "
       pdb=" C   GLY B  53 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.020 1.04e-02 9.25e+03 3.70e+00
  bond pdb=" CA  GLY A  53 "
       pdb=" C   GLY A  53 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.020 1.04e-02 9.25e+03 3.66e+00
  ... (remaining 11677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 15136
        2.07 -     4.13: 535
        4.13 -     6.20: 79
        6.20 -     8.26: 15
        8.26 -    10.33: 15
  Bond angle restraints: 15780
  Sorted by residual:
  angle pdb=" C   VAL B 215 "
        pdb=" N   ASN B 216 "
        pdb=" CA  ASN B 216 "
      ideal   model   delta    sigma   weight residual
     121.54  130.93   -9.39 1.91e+00 2.74e-01 2.42e+01
  angle pdb=" C   VAL A 215 "
        pdb=" N   ASN A 216 "
        pdb=" CA  ASN A 216 "
      ideal   model   delta    sigma   weight residual
     121.54  130.90   -9.36 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   VAL C 215 "
        pdb=" N   ASN C 216 "
        pdb=" CA  ASN C 216 "
      ideal   model   delta    sigma   weight residual
     121.54  130.90   -9.36 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" N   GLY B 349 "
        pdb=" CA  GLY B 349 "
        pdb=" C   GLY B 349 "
      ideal   model   delta    sigma   weight residual
     110.66  118.04   -7.38 1.90e+00 2.77e-01 1.51e+01
  angle pdb=" N   GLY A 349 "
        pdb=" CA  GLY A 349 "
        pdb=" C   GLY A 349 "
      ideal   model   delta    sigma   weight residual
     110.66  118.02   -7.36 1.90e+00 2.77e-01 1.50e+01
  ... (remaining 15775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 6679
       15.88 -    31.76: 332
       31.76 -    47.63: 93
       47.63 -    63.51: 30
       63.51 -    79.39: 15
  Dihedral angle restraints: 7149
    sinusoidal: 3021
      harmonic: 4128
  Sorted by residual:
  dihedral pdb=" CA  ASN B 397 "
           pdb=" C   ASN B 397 "
           pdb=" N   GLU B 398 "
           pdb=" CA  GLU B 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.08   45.92     0      5.00e+00 4.00e-02 8.43e+01
  dihedral pdb=" CA  ASN A 397 "
           pdb=" C   ASN A 397 "
           pdb=" N   GLU A 398 "
           pdb=" CA  GLU A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.11   45.89     0      5.00e+00 4.00e-02 8.42e+01
  dihedral pdb=" CA  ASN C 397 "
           pdb=" C   ASN C 397 "
           pdb=" N   GLU C 398 "
           pdb=" CA  GLU C 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.13   45.87     0      5.00e+00 4.00e-02 8.42e+01
  ... (remaining 7146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1373
       0.066 -    0.132: 296
       0.132 -    0.198: 38
       0.198 -    0.264: 14
       0.264 -    0.330: 7
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CB  ILE B 281 "
            pdb=" CA  ILE B 281 "
            pdb=" CG1 ILE B 281 "
            pdb=" CG2 ILE B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CB  ILE A 281 "
            pdb=" CA  ILE A 281 "
            pdb=" CG1 ILE A 281 "
            pdb=" CG2 ILE A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CB  ILE C 281 "
            pdb=" CA  ILE C 281 "
            pdb=" CG1 ILE C 281 "
            pdb=" CG2 ILE C 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 1725 not shown)

  Planarity restraints: 2094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 143 "   -0.025 2.00e-02 2.50e+03   1.76e-02 7.76e+00
        pdb=" CG  TRP B 143 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 143 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 143 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 143 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 143 "    0.024 2.00e-02 2.50e+03   1.76e-02 7.73e+00
        pdb=" CG  TRP A 143 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 143 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 143 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 143 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 143 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 143 "   -0.024 2.00e-02 2.50e+03   1.75e-02 7.69e+00
        pdb=" CG  TRP C 143 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 143 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 143 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 143 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2091 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 9
        2.28 -     2.93: 4636
        2.93 -     3.59: 14772
        3.59 -     4.24: 25585
        4.24 -     4.90: 42760
  Nonbonded interactions: 87762
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 453 "
            pdb=" OE1 GLU B 457 "
     model   vdw
     1.625 3.120
  nonbonded pdb=" OE1 GLU A 457 "
            pdb=" NH2 ARG C 453 "
     model   vdw
     1.625 3.120
  nonbonded pdb=" NH2 ARG B 453 "
            pdb=" OE1 GLU C 457 "
     model   vdw
     1.625 3.120
  nonbonded pdb=" NH2 ARG A 212 "
            pdb=" NE2 GLN C 202 "
     model   vdw
     2.083 3.200
  nonbonded pdb=" NE2 GLN A 202 "
            pdb=" NH2 ARG B 212 "
     model   vdw
     2.084 3.200
  ... (remaining 87757 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.200
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.300
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6132
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  11709  Z= 0.271
  Angle     :  0.968  13.496  15843  Z= 0.521
  Chirality :  0.061   0.330   1728
  Planarity :  0.005   0.048   2085
  Dihedral  : 11.603  79.385   4455
  Min Nonbonded Distance : 1.625

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.15 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.55 (0.16), residues: 1440
  helix: -4.69 (0.09), residues: 297
  sheet: -2.14 (0.27), residues: 336
  loop : -2.78 (0.16), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP B 143 
 HIS   0.010   0.002   HIS C 468 
 PHE   0.040   0.005   PHE B 251 
 TYR   0.028   0.003   TYR B 274 
 ARG   0.008   0.001   ARG B 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00620 (    9)
  link_NAG-ASN         : angle       5.31373 (   27)
  hydrogen bonds       : bond        0.32043 (  354)
  hydrogen bonds       : angle       9.78013 (  981)
  SS BOND              : bond        0.00315 (   18)
  SS BOND              : angle       1.39769 (   36)
  covalent geometry    : bond        0.00596 (11682)
  covalent geometry    : angle       0.94284 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 339
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
REVERT: B  382 ILE cc_start: 0.6813 (mm) cc_final: 0.6541 (pt)
REVERT: C  407 ILE cc_start: 0.5486 (mt) cc_final: 0.5233 (mt)
  outliers start: 6
  outliers final: 1
  residues processed: 343
  average time/residue: 0.2673
  time to fit residues: 124.0987
Evaluate side-chains
  161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0030
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
A  54 GLN
A 147 ASN
A 202 GLN
** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
B   8 HIS
B 288 ASN
** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 ASN
C   8 HIS
C  13 ASN
C  95 ASN
C 147 ASN
C 175 HIS
C 202 GLN
C 264 GLN
C 288 ASN
C 338 ASN
C 394 ASN
C 451 GLN
C 455 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.153099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.135359 restraints weight = 16035.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.38
r_work: 0.3577 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.6101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11709  Z= 0.201
  Angle     :  0.843  12.750  15843  Z= 0.428
  Chirality :  0.052   0.535   1728
  Planarity :  0.006   0.073   2085
  Dihedral  :  7.821  58.856   1766
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  :  9.11 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.18), residues: 1440
  helix: -2.32 (0.24), residues: 291
  sheet: -1.60 (0.27), residues: 342
  loop : -2.47 (0.16), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP C 143 
 HIS   0.007   0.002   HIS B   9 
 PHE   0.025   0.003   PHE C 205 
 TYR   0.014   0.002   TYR A 274 
 ARG   0.014   0.001   ARG C 479 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    9)
  link_NAG-ASN         : angle       3.18995 (   27)
  hydrogen bonds       : bond        0.06441 (  354)
  hydrogen bonds       : angle       5.34996 (  981)
  SS BOND              : bond        0.00790 (   18)
  SS BOND              : angle       1.72004 (   36)
  covalent geometry    : bond        0.00438 (11682)
  covalent geometry    : angle       0.83010 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 202
  time to evaluate  : 1.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: A  493 MET cc_start: 0.6405 (mtt) cc_final: 0.6192 (mmm)
REVERT: B  441 MET cc_start: 0.7960 (tpt) cc_final: 0.7713 (tpt)
REVERT: B  493 MET cc_start: 0.6864 (tpp) cc_final: 0.6540 (mmm)
REVERT: C   41 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7480 (mtm110)
REVERT: C  222 ILE cc_start: 0.7744 (mt) cc_final: 0.7310 (mt)
REVERT: C  371 ILE cc_start: 0.8522 (pt) cc_final: 0.8090 (mt)
REVERT: C  378 LEU cc_start: 0.7986 (mp) cc_final: 0.7672 (tt)
REVERT: C  412 ASP cc_start: 0.7803 (m-30) cc_final: 0.7480 (m-30)
REVERT: C  441 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8054 (tpp)
  outliers start: 48
  outliers final: 17
  residues processed: 242
  average time/residue: 0.2616
  time to fit residues: 87.3326
Evaluate side-chains
  130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  142 LYS
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  228 ILE
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  403 ILE
Chi-restraints excluded: chain C residue  441 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 132 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 451 GLN
B 288 ASN
B 352 HIS
B 432 HIS
B 451 GLN
C 264 GLN
C 368 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113773 restraints weight = 16222.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.31
r_work: 0.3280 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.8710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  11709  Z= 0.245
  Angle     :  0.806  11.965  15843  Z= 0.408
  Chirality :  0.053   0.455   1728
  Planarity :  0.004   0.035   2085
  Dihedral  :  7.718  59.895   1764
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 11.79 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.19), residues: 1440
  helix: -0.78 (0.28), residues: 297
  sheet: -1.38 (0.27), residues: 342
  loop : -2.29 (0.17), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP B 143 
 HIS   0.010   0.002   HIS B   9 
 PHE   0.022   0.003   PHE B 116 
 TYR   0.021   0.002   TYR B 364 
 ARG   0.008   0.001   ARG B 248 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    9)
  link_NAG-ASN         : angle       4.36302 (   27)
  hydrogen bonds       : bond        0.08020 (  354)
  hydrogen bonds       : angle       4.71742 (  981)
  SS BOND              : bond        0.00666 (   18)
  SS BOND              : angle       2.34893 (   36)
  covalent geometry    : bond        0.00595 (11682)
  covalent geometry    : angle       0.77957 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 157
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.8320 (pp) cc_final: 0.8114 (pp)
REVERT: A  268 ASN cc_start: 0.8345 (m-40) cc_final: 0.8018 (m-40)
REVERT: A  454 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: A  493 MET cc_start: 0.6983 (mtt) cc_final: 0.6451 (mmm)
REVERT: B  105 GLU cc_start: 0.8324 (pp20) cc_final: 0.7892 (pp20)
REVERT: B  141 MET cc_start: 0.8883 (mtt) cc_final: 0.8610 (mtt)
REVERT: B  161 LYS cc_start: 0.8906 (tttm) cc_final: 0.8575 (ttmm)
REVERT: B  428 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8147 (mtp)
REVERT: B  431 GLN cc_start: 0.8529 (tp40) cc_final: 0.8323 (tp40)
REVERT: B  493 MET cc_start: 0.8049 (tpp) cc_final: 0.7551 (mmm)
REVERT: B  494 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7224 (mp10)
REVERT: C  156 MET cc_start: 0.7607 (mmt) cc_final: 0.6869 (mtm)
  outliers start: 58
  outliers final: 39
  residues processed: 200
  average time/residue: 0.2471
  time to fit residues: 71.7994
Evaluate side-chains
  151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 111
  time to evaluate  : 2.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ILE
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  436 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 99 optimal weight:    0.4980
   chunk 105 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 115 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
C 264 GLN
C 356 GLN
C 431 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.134207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.116150 restraints weight = 16065.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.29
r_work: 0.3309 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.9057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11709  Z= 0.133
  Angle     :  0.640  12.325  15843  Z= 0.320
  Chirality :  0.049   0.540   1728
  Planarity :  0.003   0.032   2085
  Dihedral  :  7.018  58.471   1764
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 13.41 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.20), residues: 1440
  helix:  0.22 (0.30), residues: 294
  sheet: -1.04 (0.27), residues: 342
  loop : -2.08 (0.18), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 409 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.014   0.002   PHE C 335 
 TYR   0.019   0.001   TYR B 364 
 ARG   0.006   0.000   ARG A 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00666 (    9)
  link_NAG-ASN         : angle       4.61631 (   27)
  hydrogen bonds       : bond        0.05819 (  354)
  hydrogen bonds       : angle       4.33897 (  981)
  SS BOND              : bond        0.00628 (   18)
  SS BOND              : angle       2.15826 (   36)
  covalent geometry    : bond        0.00300 (11682)
  covalent geometry    : angle       0.60381 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 117
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.8199 (pp) cc_final: 0.7994 (pp)
REVERT: A  268 ASN cc_start: 0.8438 (m-40) cc_final: 0.8161 (m-40)
REVERT: A  389 PHE cc_start: 0.8617 (m-80) cc_final: 0.8288 (m-10)
REVERT: B   31 THR cc_start: 0.8603 (m) cc_final: 0.8344 (p)
REVERT: B  105 GLU cc_start: 0.8382 (pp20) cc_final: 0.8031 (pm20)
REVERT: B  161 LYS cc_start: 0.8866 (tttm) cc_final: 0.8610 (ttmm)
REVERT: B  372 ASP cc_start: 0.8444 (t70) cc_final: 0.8087 (m-30)
REVERT: B  398 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7258 (pt0)
REVERT: B  412 ASP cc_start: 0.8442 (m-30) cc_final: 0.7979 (m-30)
REVERT: B  428 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8122 (mtp)
REVERT: B  493 MET cc_start: 0.7847 (tpp) cc_final: 0.7556 (mmt)
REVERT: C  131 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7483 (mtp85)
REVERT: C  156 MET cc_start: 0.7608 (mmt) cc_final: 0.7216 (mpp)
REVERT: C  296 LYS cc_start: 0.8385 (mttt) cc_final: 0.7997 (mptt)
REVERT: C  444 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8829 (tp)
  outliers start: 48
  outliers final: 30
  residues processed: 151
  average time/residue: 0.2334
  time to fit residues: 51.2558
Evaluate side-chains
  134 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  356 GLN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  444 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0060
   chunk 132 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 264 GLN
C 264 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.131973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113245 restraints weight = 15975.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.35
r_work: 0.3273 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.9352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11709  Z= 0.155
  Angle     :  0.657  14.325  15843  Z= 0.329
  Chirality :  0.049   0.497   1728
  Planarity :  0.003   0.031   2085
  Dihedral  :  6.946  59.655   1764
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 13.74 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.20), residues: 1440
  helix:  0.72 (0.31), residues: 294
  sheet: -0.81 (0.28), residues: 342
  loop : -1.99 (0.18), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 409 
 HIS   0.005   0.001   HIS B   9 
 PHE   0.013   0.002   PHE A 335 
 TYR   0.018   0.001   TYR B 187 
 ARG   0.006   0.000   ARG C 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00491 (    9)
  link_NAG-ASN         : angle       4.47648 (   27)
  hydrogen bonds       : bond        0.06077 (  354)
  hydrogen bonds       : angle       4.30841 (  981)
  SS BOND              : bond        0.00573 (   18)
  SS BOND              : angle       2.52352 (   36)
  covalent geometry    : bond        0.00364 (11682)
  covalent geometry    : angle       0.62018 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 111
  time to evaluate  : 1.954 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.8217 (pp) cc_final: 0.8011 (pp)
REVERT: A  268 ASN cc_start: 0.8363 (m-40) cc_final: 0.8025 (m-40)
REVERT: B  105 GLU cc_start: 0.8367 (pp20) cc_final: 0.7944 (pm20)
REVERT: B  140 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7376 (pp20)
REVERT: B  161 LYS cc_start: 0.8979 (tttm) cc_final: 0.8680 (ttmm)
REVERT: B  398 GLU cc_start: 0.7755 (tp30) cc_final: 0.7301 (pt0)
REVERT: B  412 ASP cc_start: 0.8597 (m-30) cc_final: 0.8168 (m-30)
REVERT: B  428 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8186 (mtp)
REVERT: C  131 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7585 (mtp85)
REVERT: C  185 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7544 (tmtt)
REVERT: C  296 LYS cc_start: 0.8492 (mttt) cc_final: 0.8024 (mmtm)
REVERT: C  431 GLN cc_start: 0.8641 (tp40) cc_final: 0.8417 (tp-100)
REVERT: C  444 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8799 (tp)
  outliers start: 51
  outliers final: 41
  residues processed: 143
  average time/residue: 0.3031
  time to fit residues: 61.5430
Evaluate side-chains
  144 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  140 GLU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  475 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 121 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 139 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
C 264 GLN
C 394 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112947 restraints weight = 16139.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.36
r_work: 0.3275 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.9571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11709  Z= 0.145
  Angle     :  0.637  14.004  15843  Z= 0.319
  Chirality :  0.048   0.447   1728
  Planarity :  0.003   0.029   2085
  Dihedral  :  6.813  59.628   1764
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 13.98 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.21), residues: 1440
  helix:  1.05 (0.30), residues: 294
  sheet: -0.73 (0.28), residues: 327
  loop : -1.82 (0.18), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.012   0.002   PHE C 335 
 TYR   0.017   0.001   TYR B 364 
 ARG   0.006   0.000   ARG C 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00732 (    9)
  link_NAG-ASN         : angle       4.17535 (   27)
  hydrogen bonds       : bond        0.05846 (  354)
  hydrogen bonds       : angle       4.27354 (  981)
  SS BOND              : bond        0.00556 (   18)
  SS BOND              : angle       2.71695 (   36)
  covalent geometry    : bond        0.00337 (11682)
  covalent geometry    : angle       0.60032 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 105
  time to evaluate  : 2.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 ASN cc_start: 0.8357 (m-40) cc_final: 0.8021 (m-40)
REVERT: A  428 MET cc_start: 0.8259 (ttm) cc_final: 0.7973 (mtp)
REVERT: B  105 GLU cc_start: 0.8413 (pp20) cc_final: 0.8092 (pm20)
REVERT: B  150 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6211 (t0)
REVERT: B  161 LYS cc_start: 0.8970 (tttm) cc_final: 0.8767 (ttmm)
REVERT: B  398 GLU cc_start: 0.7658 (tp30) cc_final: 0.7285 (pt0)
REVERT: B  428 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8159 (mtp)
REVERT: C    6 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: C  131 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7593 (mtp85)
REVERT: C  296 LYS cc_start: 0.8524 (mttt) cc_final: 0.8059 (mmtm)
REVERT: C  372 ASP cc_start: 0.8418 (t70) cc_final: 0.8170 (m-30)
REVERT: C  431 GLN cc_start: 0.8604 (tp40) cc_final: 0.8380 (tp-100)
REVERT: C  444 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8815 (tp)
  outliers start: 56
  outliers final: 40
  residues processed: 143
  average time/residue: 0.3104
  time to fit residues: 67.7788
Evaluate side-chains
  145 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 2.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 143 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
C 264 GLN
C 288 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.112791 restraints weight = 16123.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.36
r_work: 0.3271 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.9676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11709  Z= 0.139
  Angle     :  0.627  13.655  15843  Z= 0.312
  Chirality :  0.047   0.412   1728
  Planarity :  0.003   0.029   2085
  Dihedral  :  6.751  58.312   1764
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 14.15 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.21), residues: 1440
  helix:  1.35 (0.30), residues: 294
  sheet: -0.45 (0.30), residues: 312
  loop : -1.76 (0.18), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.012   0.001   PHE A 335 
 TYR   0.016   0.001   TYR B 364 
 ARG   0.006   0.000   ARG C 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00495 (    9)
  link_NAG-ASN         : angle       4.16609 (   27)
  hydrogen bonds       : bond        0.05788 (  354)
  hydrogen bonds       : angle       4.26005 (  981)
  SS BOND              : bond        0.00472 (   18)
  SS BOND              : angle       2.73230 (   36)
  covalent geometry    : bond        0.00324 (11682)
  covalent geometry    : angle       0.58944 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 104
  time to evaluate  : 1.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8317 (pp)
REVERT: A  268 ASN cc_start: 0.8407 (m-40) cc_final: 0.8073 (m-40)
REVERT: A  428 MET cc_start: 0.8281 (ttm) cc_final: 0.7931 (mtp)
REVERT: B  150 ASN cc_start: 0.6450 (OUTLIER) cc_final: 0.6184 (t0)
REVERT: B  161 LYS cc_start: 0.9002 (tttm) cc_final: 0.8774 (ttmm)
REVERT: B  398 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7229 (pt0)
REVERT: B  428 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8039 (mtp)
REVERT: C    6 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8542 (pp)
REVERT: C  131 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7557 (mtp85)
REVERT: C  296 LYS cc_start: 0.8529 (mttt) cc_final: 0.8055 (mmtm)
REVERT: C  372 ASP cc_start: 0.8429 (t70) cc_final: 0.8156 (m-30)
REVERT: C  444 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8806 (tp)
REVERT: C  493 MET cc_start: 0.7667 (mmp) cc_final: 0.7262 (mmm)
  outliers start: 57
  outliers final: 42
  residues processed: 141
  average time/residue: 0.2933
  time to fit residues: 60.0842
Evaluate side-chains
  149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 101
  time to evaluate  : 1.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  475 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 137 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 133 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 203 GLN
B 232 ASN
C 264 GLN
C 288 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112840 restraints weight = 16037.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.35
r_work: 0.3273 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.9774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11709  Z= 0.139
  Angle     :  0.615  12.534  15843  Z= 0.309
  Chirality :  0.047   0.415   1728
  Planarity :  0.003   0.029   2085
  Dihedral  :  6.728  57.555   1764
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 14.72 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.21), residues: 1440
  helix:  1.58 (0.30), residues: 294
  sheet: -0.33 (0.30), residues: 312
  loop : -1.68 (0.19), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.012   0.001   PHE A 335 
 TYR   0.016   0.001   TYR B 364 
 ARG   0.007   0.000   ARG C 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00644 (    9)
  link_NAG-ASN         : angle       4.01138 (   27)
  hydrogen bonds       : bond        0.05737 (  354)
  hydrogen bonds       : angle       4.21875 (  981)
  SS BOND              : bond        0.00427 (   18)
  SS BOND              : angle       2.72639 (   36)
  covalent geometry    : bond        0.00322 (11682)
  covalent geometry    : angle       0.57950 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 107
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8337 (pp)
REVERT: A  268 ASN cc_start: 0.8412 (m-40) cc_final: 0.8064 (m-40)
REVERT: A  428 MET cc_start: 0.8296 (ttm) cc_final: 0.7984 (mtp)
REVERT: B  150 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6219 (t0)
REVERT: B  161 LYS cc_start: 0.9009 (tttm) cc_final: 0.8775 (ttmm)
REVERT: B  372 ASP cc_start: 0.8509 (t70) cc_final: 0.8161 (m-30)
REVERT: B  398 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7207 (pt0)
REVERT: B  428 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8095 (mtp)
REVERT: C  131 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7331 (mtp85)
REVERT: C  296 LYS cc_start: 0.8525 (mttt) cc_final: 0.8045 (mmtm)
REVERT: C  372 ASP cc_start: 0.8443 (t70) cc_final: 0.8171 (m-30)
REVERT: C  431 GLN cc_start: 0.8602 (tp40) cc_final: 0.8381 (tp-100)
REVERT: C  444 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8779 (tp)
REVERT: C  493 MET cc_start: 0.7697 (mmp) cc_final: 0.7317 (mmm)
  outliers start: 53
  outliers final: 43
  residues processed: 143
  average time/residue: 0.3455
  time to fit residues: 75.2938
Evaluate side-chains
  151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 103
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   chunk 126 optimal weight:    0.8980
   chunk 83 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 232 ASN
C 232 ASN
C 264 GLN
C 288 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.131141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112386 restraints weight = 16087.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.35
r_work: 0.3266 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.9854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11709  Z= 0.149
  Angle     :  0.628  11.728  15843  Z= 0.317
  Chirality :  0.047   0.386   1728
  Planarity :  0.003   0.037   2085
  Dihedral  :  6.783  57.850   1764
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 15.28 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.21), residues: 1440
  helix:  1.67 (0.30), residues: 294
  sheet: -0.43 (0.29), residues: 327
  loop : -1.61 (0.19), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.005   0.001   HIS B   9 
 PHE   0.012   0.001   PHE A 335 
 TYR   0.016   0.001   TYR B 364 
 ARG   0.009   0.000   ARG B 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00712 (    9)
  link_NAG-ASN         : angle       3.93830 (   27)
  hydrogen bonds       : bond        0.05837 (  354)
  hydrogen bonds       : angle       4.24619 (  981)
  SS BOND              : bond        0.00470 (   18)
  SS BOND              : angle       2.67839 (   36)
  covalent geometry    : bond        0.00351 (11682)
  covalent geometry    : angle       0.59425 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 105
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8335 (pp)
REVERT: A  268 ASN cc_start: 0.8418 (m-40) cc_final: 0.8078 (m-40)
REVERT: A  428 MET cc_start: 0.8307 (ttm) cc_final: 0.7992 (mtp)
REVERT: B  150 ASN cc_start: 0.6016 (OUTLIER) cc_final: 0.5700 (t0)
REVERT: B  161 LYS cc_start: 0.9029 (tttm) cc_final: 0.8784 (ttmm)
REVERT: B  372 ASP cc_start: 0.8517 (t70) cc_final: 0.8178 (m-30)
REVERT: B  398 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7280 (pm20)
REVERT: B  428 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8099 (mtp)
REVERT: C  131 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7546 (mtp85)
REVERT: C  296 LYS cc_start: 0.8553 (mttt) cc_final: 0.8064 (mmtm)
REVERT: C  372 ASP cc_start: 0.8427 (t70) cc_final: 0.8169 (m-30)
REVERT: C  431 GLN cc_start: 0.8607 (tp40) cc_final: 0.8355 (tp-100)
REVERT: C  444 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8836 (tp)
REVERT: C  493 MET cc_start: 0.7729 (mmp) cc_final: 0.7351 (mmm)
  outliers start: 53
  outliers final: 45
  residues processed: 140
  average time/residue: 0.2295
  time to fit residues: 47.2686
Evaluate side-chains
  150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 100
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  257 MET
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  475 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 112 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 175 HIS
B 232 ASN
C 232 ASN
C 288 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.131241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.112623 restraints weight = 15958.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.34
r_work: 0.3268 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.9906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11709  Z= 0.140
  Angle     :  0.616  11.387  15843  Z= 0.311
  Chirality :  0.047   0.374   1728
  Planarity :  0.003   0.041   2085
  Dihedral  :  6.733  57.294   1764
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 15.61 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.21), residues: 1440
  helix:  1.79 (0.30), residues: 294
  sheet: -0.31 (0.30), residues: 312
  loop : -1.60 (0.19), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.004   0.001   HIS B   9 
 PHE   0.012   0.001   PHE A 335 
 TYR   0.022   0.001   TYR B 187 
 ARG   0.010   0.000   ARG B 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00733 (    9)
  link_NAG-ASN         : angle       3.88901 (   27)
  hydrogen bonds       : bond        0.05738 (  354)
  hydrogen bonds       : angle       4.23399 (  981)
  SS BOND              : bond        0.00432 (   18)
  SS BOND              : angle       2.61835 (   36)
  covalent geometry    : bond        0.00323 (11682)
  covalent geometry    : angle       0.58262 (15780)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 107
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8322 (pp)
REVERT: A  268 ASN cc_start: 0.8427 (m-40) cc_final: 0.8086 (m-40)
REVERT: A  428 MET cc_start: 0.8246 (ttm) cc_final: 0.7967 (mtp)
REVERT: B  105 GLU cc_start: 0.8448 (pp20) cc_final: 0.8151 (pm20)
REVERT: B  150 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6162 (t0)
REVERT: B  161 LYS cc_start: 0.9032 (tttm) cc_final: 0.8785 (ttmm)
REVERT: B  372 ASP cc_start: 0.8502 (t70) cc_final: 0.8176 (m-30)
REVERT: B  398 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7262 (pm20)
REVERT: B  428 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8104 (mtp)
REVERT: C  131 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7421 (mtp85)
REVERT: C  156 MET cc_start: 0.7414 (mpp) cc_final: 0.7206 (mtm)
REVERT: C  296 LYS cc_start: 0.8548 (mttt) cc_final: 0.8070 (mmtm)
REVERT: C  372 ASP cc_start: 0.8432 (t70) cc_final: 0.8180 (m-30)
REVERT: C  431 GLN cc_start: 0.8606 (tp40) cc_final: 0.8358 (tp-100)
REVERT: C  444 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8839 (tp)
REVERT: C  493 MET cc_start: 0.7727 (mmp) cc_final: 0.7350 (mmm)
  outliers start: 49
  outliers final: 44
  residues processed: 140
  average time/residue: 0.2360
  time to fit residues: 47.7006
Evaluate side-chains
  150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  257 MET
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  428 MET
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  463 CYS
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    9 HIS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  312 MET
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  381 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  475 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0060
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1000

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 232 ASN
C 232 ASN
C 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.129759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111128 restraints weight = 16008.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.34
r_work: 0.3233 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.9965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11709  Z= 0.170
  Angle     :  0.648  12.285  15843  Z= 0.326
  Chirality :  0.048   0.373   1728
  Planarity :  0.003   0.041   2085
  Dihedral  :  6.938  59.875   1764
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.69 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.21), residues: 1440
  helix:  1.74 (0.30), residues: 294
  sheet: -0.46 (0.29), residues: 327
  loop : -1.55 (0.19), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 409 
 HIS   0.005   0.001   HIS B   9 
 PHE   0.012   0.002   PHE A 116 
 TYR   0.021   0.002   TYR B 187 
 ARG   0.010   0.001   ARG B 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00721 (    9)
  link_NAG-ASN         : angle       3.88037 (   27)
  hydrogen bonds       : bond        0.06090 (  354)
  hydrogen bonds       : angle       4.28141 (  981)
  SS BOND              : bond        0.00481 (   18)
  SS BOND              : angle       2.70765 (   36)
  covalent geometry    : bond        0.00405 (11682)
  covalent geometry    : angle       0.61591 (15780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5938.16 seconds
wall clock time: 108 minutes 59.58 seconds (6539.58 seconds total)