Starting phenix.real_space_refine
on Wed Mar  4 00:00:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2026/7qo9_14087.map"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      45      5.16       5
     C    5830      2.51       5
     N    1523      2.21       5
     O    1782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9180
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4568
          Classifications: {'peptide': 588}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 25, 'TRANS': 562}
          Chain breaks: 14
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 4486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4486
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 26, 'TRANS': 551}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 31
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2, 'water': 3}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.07, per 1000 atoms: 0.23
  Number of scatterers: 9180
  At special positions: 0
  Unit cell: (87.5022, 112.046, 122.717, 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      45     16.00
     O    1782      8.00
     N    1523      7.00
     C    5830      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 161 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 614 " - pdb=" SG  CYS A 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 659 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 735 " - pdb=" SG  CYS A 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 740 " - pdb=" SG  CYS A 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 485 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 535 " - pdb=" SG  CYS B 587 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 659 " - pdb=" SG  CYS B 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 735 " - pdb=" SG  CYS B 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 740 " - pdb=" SG  CYS B 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 837 " - pdb=" SG  CYS B 848 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 231 "
      " NAG A1302 " - " ASN A 279 "
      " NAG C   1 " - " ASN A 160 "
      " NAG D   1 " - " ASN A 120 "
      " NAG E   1 " - " ASN A 135 "
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 358.6 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2188

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 17 sheets defined
      26.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 73
    Processing helix  chain 'A' and resid 291 through 301
    Processing helix  chain 'A' and resid 619 through 624
    Processing helix  chain 'A' and resid 734 through 740
      removed outlier: 3.661A  pdb=" N   TYR A 738 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 752
      removed outlier: 3.500A  pdb=" N   GLN A 752 " --> pdb=" O   ASN A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 780
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 3.589A  pdb=" N   PHE A 852 " --> pdb=" O   CYS A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 874
    Processing helix  chain 'A' and resid 943 through 962
      removed outlier: 4.873A  pdb=" N   VAL A 948 " --> pdb=" O   LYS A 944 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 949 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 965
      No H-bonds generated for 'chain 'A' and resid 963 through 965'
    Processing helix  chain 'A' and resid 973 through 981
    Processing helix  chain 'A' and resid 982 through 1022
      removed outlier: 4.599A  pdb=" N   VAL A 988 " --> pdb=" O   PRO A 984 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 993 " --> pdb=" O   GLN A 989 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 368
      removed outlier: 3.769A  pdb=" N   TYR B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 387
      removed outlier: 3.762A  pdb=" N   LEU B 384 " --> pdb=" O   PRO B 381 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN B 385 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU B 387 " --> pdb=" O   LEU B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 734 through 739
    Processing helix  chain 'B' and resid 743 through 751
    Processing helix  chain 'B' and resid 752 through 754
      No H-bonds generated for 'chain 'B' and resid 752 through 754'
    Processing helix  chain 'B' and resid 757 through 779
      removed outlier: 3.565A  pdb=" N   ILE B 767 " --> pdb=" O   ALA B 763 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS B 773 " --> pdb=" O   VAL B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 824
    Processing helix  chain 'B' and resid 825 through 827
      No H-bonds generated for 'chain 'B' and resid 825 through 827'
    Processing helix  chain 'B' and resid 863 through 864
      No H-bonds generated for 'chain 'B' and resid 863 through 864'
    Processing helix  chain 'B' and resid 866 through 868
      No H-bonds generated for 'chain 'B' and resid 866 through 868'
    Processing helix  chain 'B' and resid 942 through 962
      removed outlier: 3.739A  pdb=" N   GLN B 946 " --> pdb=" O   LEU B 942 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 948 " --> pdb=" O   LYS B 944 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 949 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 963 through 965
      No H-bonds generated for 'chain 'B' and resid 963 through 965'
    Processing helix  chain 'B' and resid 973 through 980
    Processing helix  chain 'B' and resid 982 through 1022
      removed outlier: 4.466A  pdb=" N   VAL B 988 " --> pdb=" O   PRO B 984 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37
      removed outlier: 7.205A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   SER A 200 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55
      removed outlier: 4.508A  pdb=" N   ASP A 284 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68
    Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105
      removed outlier: 3.861A  pdb=" N   SER A 114 " --> pdb=" O   CYS A 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS A 129 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE A 126 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   VAL A 128 " --> pdb=" O   CYS A 161 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   CYS A 161 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   SER A 157 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316
      removed outlier: 5.626A  pdb=" N   ILE A 309 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   THR A 596 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   GLN A 311 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL A 594 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 313 " --> pdb=" O   VAL A 592 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 591 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 657
      removed outlier: 6.058A  pdb=" N   THR A 693 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 655 " --> pdb=" O   THR A 693 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ALA A 669 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 725
    Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 733
    Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 316
      removed outlier: 3.807A  pdb=" N   THR B 312 " --> pdb=" O   VAL B 592 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   VAL B 592 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ASN B 314 " --> pdb=" O   GLY B 590 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLY B 590 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY B 591 " --> pdb=" O   GLN B 610 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 323
      removed outlier: 3.500A  pdb=" N   ASN B 539 " --> pdb=" O   ILE B 323 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE B 540 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355
      removed outlier: 3.836A  pdb=" N   VAL B 392 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359
      removed outlier: 6.547A  pdb=" N   CYS B 358 " --> pdb=" O   CYS B 522 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 434
      removed outlier: 3.708A  pdb=" N   ARG B 506 " --> pdb=" O   TRP B 433 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 651 through 652
      removed outlier: 6.593A  pdb=" N   GLU B 651 " --> pdb=" O   ALA B 691 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   THR B 693 " --> pdb=" O   GLU B 651 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 732 through 733

    300 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1899
        1.33 -     1.45: 2235
        1.45 -     1.58: 5160
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 9349
  Sorted by residual:
  bond pdb=" N   GLN A 625 "
       pdb=" CA  GLN A 625 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.29e-02 6.01e+03 1.31e+01
  bond pdb=" CA  SER B 491 "
       pdb=" CB  SER B 491 "
    ideal  model  delta    sigma   weight residual
    1.530  1.480  0.050 1.39e-02 5.18e+03 1.30e+01
  bond pdb=" N   VAL B 480 "
       pdb=" CA  VAL B 480 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.045 1.25e-02 6.40e+03 1.29e+01
  bond pdb=" N   ASP A 624 "
       pdb=" CA  ASP A 624 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.20e-02 6.94e+03 9.24e+00
  bond pdb=" N   CYS B 485 "
       pdb=" CA  CYS B 485 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.26e-02 6.30e+03 7.82e+00
  ... (remaining 9344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 12443
        2.37 -     4.74: 203
        4.74 -     7.10: 37
        7.10 -     9.47: 3
        9.47 -    11.84: 4
  Bond angle restraints: 12690
  Sorted by residual:
  angle pdb=" N   PRO A 628 "
        pdb=" CA  PRO A 628 "
        pdb=" CB  PRO A 628 "
      ideal   model   delta    sigma   weight residual
     103.25   92.75   10.50 1.05e+00 9.07e-01 1.00e+02
  angle pdb=" C   TYR B 448 "
        pdb=" CA  TYR B 448 "
        pdb=" CB  TYR B 448 "
      ideal   model   delta    sigma   weight residual
     110.88   99.97   10.91 1.57e+00 4.06e-01 4.83e+01
  angle pdb=" C   TYR B 486 "
        pdb=" CA  TYR B 486 "
        pdb=" CB  TYR B 486 "
      ideal   model   delta    sigma   weight residual
     109.83   97.99   11.84 1.75e+00 3.27e-01 4.58e+01
  angle pdb=" C   TYR B 446 "
        pdb=" CA  TYR B 446 "
        pdb=" CB  TYR B 446 "
      ideal   model   delta    sigma   weight residual
     114.87  104.90    9.97 1.51e+00 4.39e-01 4.36e+01
  angle pdb=" CA  ASP A 624 "
        pdb=" C   ASP A 624 "
        pdb=" O   ASP A 624 "
      ideal   model   delta    sigma   weight residual
     121.31  116.01    5.30 1.07e+00 8.73e-01 2.45e+01
  ... (remaining 12685 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 5320
       23.74 -    47.48: 327
       47.48 -    71.21: 45
       71.21 -    94.95: 24
       94.95 -   118.69: 13
  Dihedral angle restraints: 5729
    sinusoidal: 2346
      harmonic: 3383
  Sorted by residual:
  dihedral pdb=" CB  CYS A 288 "
           pdb=" SG  CYS A 288 "
           pdb=" SG  CYS A 298 "
           pdb=" CB  CYS A 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.55   81.55     1      1.00e+01 1.00e-02 8.19e+01
  dihedral pdb=" CB  CYS B 535 "
           pdb=" SG  CYS B 535 "
           pdb=" SG  CYS B 587 "
           pdb=" CB  CYS B 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.51  -80.49     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" CB  CYS A 659 "
           pdb=" SG  CYS A 659 "
           pdb=" SG  CYS A 668 "
           pdb=" CB  CYS A 668 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.72  -74.28     1      1.00e+01 1.00e-02 7.00e+01
  ... (remaining 5726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1436
       0.110 -    0.219: 48
       0.219 -    0.329: 8
       0.329 -    0.438: 3
       0.438 -    0.548: 3
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CA  TYR B 448 "
            pdb=" N   TYR B 448 "
            pdb=" C   TYR B 448 "
            pdb=" CB  TYR B 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.06   -0.55 2.00e-01 2.50e+01 7.50e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 160 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.91   -0.49 2.00e-01 2.50e+01 6.12e+00
  chirality pdb=" CA  TYR B 446 "
            pdb=" N   TYR B 446 "
            pdb=" C   TYR B 446 "
            pdb=" CB  TYR B 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.96   -0.45 2.00e-01 2.50e+01 4.96e+00
  ... (remaining 1495 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 627 "    0.016 2.00e-02 2.50e+03   3.16e-02 9.99e+00
        pdb=" C   THR A 627 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 627 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A 628 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 226 "    0.043 5.00e-02 4.00e+02   6.61e-02 6.98e+00
        pdb=" N   PRO A 227 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 227 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 227 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  79 "    0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO A  80 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 528
        2.72 -     3.27: 9666
        3.27 -     3.81: 14147
        3.81 -     4.36: 16230
        4.36 -     4.90: 27275
  Nonbonded interactions: 67846
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  89 "
            pdb=" OE1 GLU A 186 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   THR B 863 "
            pdb=" N   MET B 866 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   VAL A 619 "
            pdb=" ND1 HIS A 622 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OG  SER A 110 "
            pdb=" OE1 GLN A 132 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER A 755 "
            pdb=" OG1 THR A 758 "
     model   vdw
     2.251 3.040
  ... (remaining 67841 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.510
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     9.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
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      :  0.004   0.053   9375  Z= 0.228
  Angle     :  0.777  11.839  12751  Z= 0.439
  Chirality :  0.056   0.548   1498
  Planarity :  0.005   0.066   1615
  Dihedral  : 16.656 118.691   3490
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.16 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  0.50 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.25), residues: 1124
  helix:  1.37 (0.33), residues: 272
  sheet: -0.07 (0.39), residues: 181
  loop : -2.05 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B1016 
 TYR   0.031   0.001   TYR B 450 
 PHE   0.037   0.001   PHE B 371 
 TRP   0.007   0.001   TRP B 433 
 HIS   0.004   0.001   HIS B 951 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 9349)
  covalent geometry    : angle       0.75746 (12690)
  SS BOND              : bond        0.00372 (   17)
  SS BOND              : angle       1.90374 (   34)
  hydrogen bonds       : bond        0.14730 (  300)
  hydrogen bonds       : angle       6.02204 (  819)
  link_BETA1-4         : bond        0.00785 (    4)
  link_BETA1-4         : angle       3.93467 (   12)
  link_NAG-ASN         : bond        0.00720 (    5)
  link_NAG-ASN         : angle       2.69980 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  290 LEU cc_start: 0.8808 (tt) cc_final: 0.8282 (tt)
REVERT: A  773 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8279 (tptt)
REVERT: A  774 ASN cc_start: 0.8574 (m110) cc_final: 0.8373 (m110)
REVERT: B  446 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6469 (t80)
REVERT: B  490 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7177 (tpm170)
REVERT: B  770 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6273 (tm-30)
REVERT: B  999 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7872 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 120
  average time/residue: 0.0877
  time to fit residues: 15.0191
Evaluate side-chains
  77 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  628 PRO
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  491 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0370
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.7840

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
B 962 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.116422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.091009 restraints weight = 28448.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090856 restraints weight = 18894.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.091635 restraints weight = 15008.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.092101 restraints weight = 12787.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.092259 restraints weight = 11389.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9375  Z= 0.190
  Angle     :  0.712  10.906  12751  Z= 0.359
  Chirality :  0.047   0.327   1498
  Planarity :  0.005   0.067   1615
  Dihedral  : 13.052 109.288   1434
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.05 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.82 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.25), residues: 1124
  helix:  1.44 (0.32), residues: 263
  sheet: -0.03 (0.39), residues: 172
  loop : -2.25 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 405 
 TYR   0.013   0.001   TYR B 348 
 PHE   0.021   0.002   PHE B 371 
 TRP   0.015   0.002   TRP A 630 
 HIS   0.002   0.001   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9349)
  covalent geometry    : angle       0.69507 (12690)
  SS BOND              : bond        0.00379 (   17)
  SS BOND              : angle       1.74512 (   34)
  hydrogen bonds       : bond        0.04759 (  300)
  hydrogen bonds       : angle       5.44906 (  819)
  link_BETA1-4         : bond        0.00779 (    4)
  link_BETA1-4         : angle       3.48856 (   12)
  link_NAG-ASN         : bond        0.00419 (    5)
  link_NAG-ASN         : angle       2.41646 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  629 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8082 (t)
REVERT: A  833 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7979 (tp-100)
REVERT: B  446 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6472 (t80)
REVERT: B  490 ARG cc_start: 0.8108 (mtt90) cc_final: 0.6882 (tpm170)
REVERT: B  737 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7781 (tpp)
REVERT: B  770 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6472 (tm-30)
REVERT: B  999 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7895 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8970 (mt)
  outliers start: 13
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0912
  time to fit residues: 11.5223
Evaluate side-chains
  77 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 110 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0070
   chunk 64 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.1404

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.115019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.089461 restraints weight = 28587.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089531 restraints weight = 18234.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.090334 restraints weight = 15328.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.090499 restraints weight = 13101.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090713 restraints weight = 12280.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9375  Z= 0.206
  Angle     :  0.708   9.249  12751  Z= 0.356
  Chirality :  0.047   0.357   1498
  Planarity :  0.005   0.067   1615
  Dihedral  : 12.064 113.184   1428
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.50 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.88 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.24), residues: 1124
  helix:  1.50 (0.32), residues: 263
  sheet: -0.12 (0.39), residues: 171
  loop : -2.34 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 997 
 TYR   0.012   0.001   TYR B 448 
 PHE   0.022   0.002   PHE B 556 
 TRP   0.008   0.001   TRP A 630 
 HIS   0.005   0.001   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 9349)
  covalent geometry    : angle       0.69210 (12690)
  SS BOND              : bond        0.00408 (   17)
  SS BOND              : angle       1.66429 (   34)
  hydrogen bonds       : bond        0.04667 (  300)
  hydrogen bonds       : angle       5.33676 (  819)
  link_BETA1-4         : bond        0.00836 (    4)
  link_BETA1-4         : angle       3.37712 (   12)
  link_NAG-ASN         : bond        0.00377 (    5)
  link_NAG-ASN         : angle       2.28800 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  833 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7946 (tp-100)
REVERT: B  415 ILE cc_start: 0.8384 (mp) cc_final: 0.7881 (tp)
REVERT: B  446 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6600 (t80)
REVERT: B  490 ARG cc_start: 0.8179 (mtt90) cc_final: 0.6940 (tpm170)
REVERT: B  770 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6772 (tp30)
REVERT: B  999 GLN cc_start: 0.8591 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8958 (mt)
  outliers start: 20
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0908
  time to fit residues: 11.8736
Evaluate side-chains
  74 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:    0.3980
   chunk 106 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.117090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.092037 restraints weight = 28464.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.091544 restraints weight = 18499.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.092467 restraints weight = 14258.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.093095 restraints weight = 11929.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093222 restraints weight = 10904.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9375  Z= 0.120
  Angle     :  0.647   9.666  12751  Z= 0.320
  Chirality :  0.045   0.349   1498
  Planarity :  0.004   0.053   1615
  Dihedral  : 11.186 111.681   1428
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.70 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.86 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.25), residues: 1124
  helix:  1.76 (0.33), residues: 263
  sheet:  0.34 (0.44), residues: 141
  loop : -2.18 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 762 
 TYR   0.011   0.001   TYR B 348 
 PHE   0.013   0.001   PHE B 371 
 TRP   0.008   0.001   TRP A 630 
 HIS   0.003   0.001   HIS B 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9349)
  covalent geometry    : angle       0.63085 (12690)
  SS BOND              : bond        0.00264 (   17)
  SS BOND              : angle       1.30019 (   34)
  hydrogen bonds       : bond        0.04009 (  300)
  hydrogen bonds       : angle       4.90170 (  819)
  link_BETA1-4         : bond        0.00882 (    4)
  link_BETA1-4         : angle       3.57505 (   12)
  link_NAG-ASN         : bond        0.00350 (    5)
  link_NAG-ASN         : angle       2.26691 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  773 LYS cc_start: 0.9144 (tptt) cc_final: 0.8382 (tptt)
REVERT: A  833 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7795 (tp-100)
REVERT: A  987 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8751 (tm-30)
REVERT: B  415 ILE cc_start: 0.8323 (mp) cc_final: 0.7787 (tp)
REVERT: B  446 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6653 (t80)
REVERT: B  490 ARG cc_start: 0.7909 (mtt90) cc_final: 0.6779 (tpm170)
REVERT: B  737 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7816 (tpp)
REVERT: B  770 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6595 (tp30)
REVERT: B  973 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8051 (m)
REVERT: B  999 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7884 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0929
  time to fit residues: 12.0715
Evaluate side-chains
  83 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 78 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 946 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.117271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.091927 restraints weight = 28468.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.092422 restraints weight = 17802.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.093003 restraints weight = 14662.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.093162 restraints weight = 12617.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.093309 restraints weight = 11759.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9375  Z= 0.121
  Angle     :  0.642  10.018  12751  Z= 0.317
  Chirality :  0.046   0.332   1498
  Planarity :  0.004   0.061   1615
  Dihedral  : 10.592 110.663   1428
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  9.88 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.64 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.25), residues: 1124
  helix:  1.66 (0.33), residues: 269
  sheet:  0.38 (0.44), residues: 141
  loop : -2.18 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 980 
 TYR   0.012   0.001   TYR B 448 
 PHE   0.013   0.001   PHE A 272 
 TRP   0.007   0.001   TRP A 630 
 HIS   0.003   0.001   HIS B 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9349)
  covalent geometry    : angle       0.62541 (12690)
  SS BOND              : bond        0.00254 (   17)
  SS BOND              : angle       1.23546 (   34)
  hydrogen bonds       : bond        0.03927 (  300)
  hydrogen bonds       : angle       4.77421 (  819)
  link_BETA1-4         : bond        0.00812 (    4)
  link_BETA1-4         : angle       3.68033 (   12)
  link_NAG-ASN         : bond        0.00320 (    5)
  link_NAG-ASN         : angle       2.18109 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  622 HIS cc_start: 0.4359 (p-80) cc_final: 0.4003 (p-80)
REVERT: A  833 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7708 (tp-100)
REVERT: A  987 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8808 (tm-30)
REVERT: B  415 ILE cc_start: 0.8403 (mp) cc_final: 0.7874 (tp)
REVERT: B  446 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6742 (t80)
REVERT: B  490 ARG cc_start: 0.7979 (mtt90) cc_final: 0.6880 (tpm170)
REVERT: B  737 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7800 (tpp)
REVERT: B  770 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6623 (tp30)
REVERT: B  999 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7901 (tm-30)
  outliers start: 26
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0874
  time to fit residues: 13.0711
Evaluate side-chains
  89 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 97 optimal weight:    0.3980
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
B1008 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.113973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.088440 restraints weight = 28860.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.088714 restraints weight = 18948.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.089072 restraints weight = 15673.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.089278 restraints weight = 13664.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089500 restraints weight = 12516.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9375  Z= 0.231
  Angle     :  0.738   9.778  12751  Z= 0.368
  Chirality :  0.047   0.316   1498
  Planarity :  0.005   0.058   1615
  Dihedral  : 10.379 110.570   1428
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.48 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.23 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.24), residues: 1124
  helix:  1.46 (0.32), residues: 269
  sheet: -0.03 (0.42), residues: 146
  loop : -2.39 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 762 
 TYR   0.012   0.002   TYR A 276 
 PHE   0.017   0.002   PHE B 556 
 TRP   0.010   0.002   TRP A 630 
 HIS   0.004   0.001   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 9349)
  covalent geometry    : angle       0.72230 (12690)
  SS BOND              : bond        0.00614 (   17)
  SS BOND              : angle       1.60258 (   34)
  hydrogen bonds       : bond        0.04583 (  300)
  hydrogen bonds       : angle       5.21846 (  819)
  link_BETA1-4         : bond        0.00891 (    4)
  link_BETA1-4         : angle       3.64297 (   12)
  link_NAG-ASN         : bond        0.00312 (    5)
  link_NAG-ASN         : angle       2.27236 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  833 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7804 (tp-100)
REVERT: A  987 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8824 (tm-30)
REVERT: B  415 ILE cc_start: 0.8410 (mp) cc_final: 0.7853 (tp)
REVERT: B  446 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6829 (t80)
REVERT: B  490 ARG cc_start: 0.8140 (mtt90) cc_final: 0.6949 (tpm170)
REVERT: B  737 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7791 (tpp)
REVERT: B  999 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8982 (mt)
  outliers start: 29
  outliers final: 19
  residues processed: 89
  average time/residue: 0.0888
  time to fit residues: 11.6408
Evaluate side-chains
  85 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 748 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.116488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.091004 restraints weight = 28588.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091272 restraints weight = 18715.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.091730 restraints weight = 15674.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.092032 restraints weight = 12965.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.092234 restraints weight = 12137.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9375  Z= 0.123
  Angle     :  0.659  10.788  12751  Z= 0.325
  Chirality :  0.045   0.323   1498
  Planarity :  0.004   0.051   1615
  Dihedral  :  9.897 107.981   1428
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.70 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.12 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.25), residues: 1124
  helix:  1.69 (0.33), residues: 269
  sheet:  0.13 (0.44), residues: 139
  loop : -2.27 (0.21), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 762 
 TYR   0.010   0.001   TYR B 348 
 PHE   0.009   0.001   PHE B 371 
 TRP   0.008   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A1055 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9349)
  covalent geometry    : angle       0.64189 (12690)
  SS BOND              : bond        0.00326 (   17)
  SS BOND              : angle       1.41728 (   34)
  hydrogen bonds       : bond        0.03988 (  300)
  hydrogen bonds       : angle       4.83953 (  819)
  link_BETA1-4         : bond        0.00825 (    4)
  link_BETA1-4         : angle       3.77735 (   12)
  link_NAG-ASN         : bond        0.00272 (    5)
  link_NAG-ASN         : angle       2.18666 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8387 (tt)
REVERT: A  773 LYS cc_start: 0.9119 (tptt) cc_final: 0.8910 (tptt)
REVERT: A  987 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8831 (tm-30)
REVERT: B  415 ILE cc_start: 0.8407 (mp) cc_final: 0.7845 (tp)
REVERT: B  446 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: B  490 ARG cc_start: 0.7981 (mtt90) cc_final: 0.6877 (tpm170)
REVERT: B  737 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7736 (tpp)
REVERT: B  752 GLN cc_start: 0.8907 (mp10) cc_final: 0.8662 (mp10)
REVERT: B  770 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7603 (tt0)
REVERT: B  999 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7899 (tm-30)
  outliers start: 27
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0932
  time to fit residues: 13.1752
Evaluate side-chains
  88 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 103 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.115872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.089809 restraints weight = 27709.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.090561 restraints weight = 16990.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.091454 restraints weight = 13052.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091639 restraints weight = 10909.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.091804 restraints weight = 10413.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9375  Z= 0.127
  Angle     :  0.667  10.970  12751  Z= 0.327
  Chirality :  0.045   0.322   1498
  Planarity :  0.004   0.060   1615
  Dihedral  :  9.576 107.576   1428
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.88 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.11 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.25), residues: 1124
  helix:  1.59 (0.33), residues: 269
  sheet:  0.15 (0.44), residues: 141
  loop : -2.28 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 762 
 TYR   0.012   0.001   TYR B 492 
 PHE   0.009   0.001   PHE A 170 
 TRP   0.010   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9349)
  covalent geometry    : angle       0.64988 (12690)
  SS BOND              : bond        0.00329 (   17)
  SS BOND              : angle       1.40476 (   34)
  hydrogen bonds       : bond        0.03936 (  300)
  hydrogen bonds       : angle       4.79253 (  819)
  link_BETA1-4         : bond        0.00762 (    4)
  link_BETA1-4         : angle       3.79059 (   12)
  link_NAG-ASN         : bond        0.00262 (    5)
  link_NAG-ASN         : angle       2.17831 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8389 (tt)
REVERT: A  773 LYS cc_start: 0.9173 (tptt) cc_final: 0.8969 (tptt)
REVERT: A  987 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8803 (tm-30)
REVERT: B  415 ILE cc_start: 0.8398 (mp) cc_final: 0.7818 (tp)
REVERT: B  490 ARG cc_start: 0.7992 (mtt90) cc_final: 0.6901 (tpm170)
REVERT: B  737 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7746 (tpp)
REVERT: B  752 GLN cc_start: 0.8911 (mp10) cc_final: 0.8673 (mp10)
REVERT: B  999 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7923 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 89
  average time/residue: 0.0883
  time to fit residues: 11.5763
Evaluate side-chains
  89 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 83 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B 962 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.116490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.091054 restraints weight = 28586.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091356 restraints weight = 18812.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.091841 restraints weight = 16108.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091908 restraints weight = 14128.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.092217 restraints weight = 12519.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9375  Z= 0.129
  Angle     :  0.661  11.751  12751  Z= 0.326
  Chirality :  0.045   0.320   1498
  Planarity :  0.004   0.050   1615
  Dihedral  :  9.227 107.381   1425
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.96 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.11 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.25), residues: 1124
  helix:  1.63 (0.33), residues: 269
  sheet:  0.16 (0.44), residues: 141
  loop : -2.27 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 762 
 TYR   0.014   0.001   TYR B 492 
 PHE   0.015   0.001   PHE A 756 
 TRP   0.009   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A1055 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9349)
  covalent geometry    : angle       0.64441 (12690)
  SS BOND              : bond        0.00327 (   17)
  SS BOND              : angle       1.45587 (   34)
  hydrogen bonds       : bond        0.03904 (  300)
  hydrogen bonds       : angle       4.74611 (  819)
  link_BETA1-4         : bond        0.00597 (    4)
  link_BETA1-4         : angle       3.75390 (   12)
  link_NAG-ASN         : bond        0.00266 (    5)
  link_NAG-ASN         : angle       2.10184 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 MET cc_start: 0.7896 (tpt) cc_final: 0.7503 (tpp)
REVERT: A  300 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8391 (tt)
REVERT: A  987 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8865 (tm-30)
REVERT: B  415 ILE cc_start: 0.8408 (mp) cc_final: 0.7847 (tp)
REVERT: B  446 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6619 (t80)
REVERT: B  490 ARG cc_start: 0.8071 (mtt90) cc_final: 0.6985 (tpm170)
REVERT: B  737 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7700 (tpp)
REVERT: B  770 GLU cc_start: 0.7919 (pt0) cc_final: 0.7534 (tt0)
REVERT: B  999 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7889 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0865
  time to fit residues: 11.5247
Evaluate side-chains
  96 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 962 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.117186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.088620 restraints weight = 28724.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.090833 restraints weight = 18112.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.092299 restraints weight = 13530.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.093239 restraints weight = 11218.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.093906 restraints weight = 9983.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9375  Z= 0.119
  Angle     :  0.666  13.380  12751  Z= 0.328
  Chirality :  0.045   0.348   1498
  Planarity :  0.004   0.047   1615
  Dihedral  :  9.015 105.905   1425
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.61 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.31 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.25), residues: 1124
  helix:  1.64 (0.34), residues: 265
  sheet:  0.26 (0.45), residues: 136
  loop : -2.25 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 762 
 TYR   0.014   0.001   TYR B 492 
 PHE   0.021   0.001   PHE A 272 
 TRP   0.010   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9349)
  covalent geometry    : angle       0.64979 (12690)
  SS BOND              : bond        0.00340 (   17)
  SS BOND              : angle       1.44226 (   34)
  hydrogen bonds       : bond        0.03735 (  300)
  hydrogen bonds       : angle       4.63356 (  819)
  link_BETA1-4         : bond        0.00595 (    4)
  link_BETA1-4         : angle       3.70597 (   12)
  link_NAG-ASN         : bond        0.00227 (    5)
  link_NAG-ASN         : angle       2.07121 (   15)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 MET cc_start: 0.7649 (tpt) cc_final: 0.7283 (tpp)
REVERT: A  272 PHE cc_start: 0.8753 (m-10) cc_final: 0.8345 (m-10)
REVERT: A  987 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8716 (tm-30)
REVERT: B  415 ILE cc_start: 0.8421 (mp) cc_final: 0.7872 (tp)
REVERT: B  446 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: B  490 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7014 (tpm170)
REVERT: B  737 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7647 (tpp)
REVERT: B  770 GLU cc_start: 0.7826 (pt0) cc_final: 0.7492 (tt0)
REVERT: B  999 GLN cc_start: 0.8575 (tm-30) cc_final: 0.7898 (tm-30)
  outliers start: 20
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0886
  time to fit residues: 11.8975
Evaluate side-chains
  93 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0040
   chunk 105 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.117107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.090637 restraints weight = 28276.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.092530 restraints weight = 18878.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.092800 restraints weight = 13648.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093243 restraints weight = 11985.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.093424 restraints weight = 11239.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9375  Z= 0.120
  Angle     :  0.659  12.199  12751  Z= 0.326
  Chirality :  0.045   0.322   1498
  Planarity :  0.004   0.055   1615
  Dihedral  :  8.937 106.010   1425
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.70 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.31 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.25), residues: 1124
  helix:  1.64 (0.33), residues: 265
  sheet:  0.27 (0.45), residues: 136
  loop : -2.23 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 762 
 TYR   0.014   0.001   TYR B 492 
 PHE   0.023   0.001   PHE A 756 
 TRP   0.014   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9349)
  covalent geometry    : angle       0.64265 (12690)
  SS BOND              : bond        0.00326 (   17)
  SS BOND              : angle       1.44869 (   34)
  hydrogen bonds       : bond        0.03703 (  300)
  hydrogen bonds       : angle       4.61409 (  819)
  link_BETA1-4         : bond        0.00578 (    4)
  link_BETA1-4         : angle       3.61517 (   12)
  link_NAG-ASN         : bond        0.00244 (    5)
  link_NAG-ASN         : angle       2.05748 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.38 seconds
wall clock time: 26 minutes 40.51 seconds (1600.51 seconds total)