Starting phenix.real_space_refine
on Wed Mar  4 22:24:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oyz_71042/03_2026/9oyz_71042.map"
  }
  resolution = 2.9
  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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5295      2.51       5
     N    1325      2.21       5
     O    1592      1.98       5
     H    7680      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 15928
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 15718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1005, 15718
          Classifications: {'peptide': 1005}
          Link IDs: {'PTRANS': 51, 'TRANS': 953}
          Chain breaks: 3
    Chain: "A"
      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: "B"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 182
          Unusual residues: {'NAG': 13}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 13
  Time building chain proxies: 2.93, per 1000 atoms: 0.18
  Number of scatterers: 15928
  At special positions: 0
  Unit cell: (95.58, 127.44, 125.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O    1592      8.00
     N    1325      7.00
     C    5295      6.00
     H    7680      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  30 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  76 " - pdb=" SG  CYS B  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 401 " - pdb=" SG  CYS B 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 864 " - pdb=" SG  CYS B 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 984 " - pdb=" SG  CYS B1000 " 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 A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN B 480 "
      " NAG B2401 " - " ASN B 123 "
      " NAG B2402 " - " ASN B 132 "
      " NAG B2403 " - " ASN B 333 "
      " NAG B2404 " - " ASN B 405 "
      " NAG B2405 " - " ASN B 607 "
      " NAG B2406 " - " ASN B 628 "
      " NAG B2407 " - " ASN B 971 "
      " NAG B2408 " - " ASN B  49 "
      " NAG B2409 " - " ASN B  65 "
      " NAG B2410 " - " ASN B 265 "
      " NAG B2411 " - " ASN B 287 "
      " NAG B2412 " - " ASN B 377 "
      " NAG B2413 " - " ASN B 714 "
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 633.4 milliseconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 23 sheets defined
      8.4% alpha, 39.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 38
    Processing helix  chain 'B' and resid 49 through 64
      removed outlier: 3.523A  pdb=" N   TRP B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 4.159A  pdb=" N   GLN B  69 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL B  70 " --> pdb=" O   THR B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 4.025A  pdb=" N   LYS B  75 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   CYS B  76 " --> pdb=" O   CYS B  72 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN B  77 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 108
    Processing helix  chain 'B' and resid 364 through 368
    Processing helix  chain 'B' and resid 563 through 567
    Processing helix  chain 'B' and resid 931 through 935
    Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 42
      removed outlier: 7.254A  pdb=" N   GLU B  41 " --> pdb=" O   VAL B 782 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ALA B 784 " --> pdb=" O   GLU B  41 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   MET B 780 " --> pdb=" O   SER B 774 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   SER B 774 " --> pdb=" O   MET B 780 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   VAL B 782 " --> pdb=" O   ARG B 772 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG B 772 " --> pdb=" O   VAL B 782 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   MET B 751 " --> pdb=" O   ALA B 764 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.806A  pdb=" N   THR B 125 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 157
      removed outlier: 5.632A  pdb=" N   TYR B 153 " --> pdb=" O   TRP B 142 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   TRP B 142 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLU B 155 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ILE B 140 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 157
      removed outlier: 5.632A  pdb=" N   TYR B 153 " --> pdb=" O   TRP B 142 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   TRP B 142 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLU B 155 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ILE B 140 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 216
      removed outlier: 4.476A  pdb=" N   SER B 223 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ILE B 212 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLU B 221 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   SER B 214 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   THR B 219 " --> pdb=" O   SER B 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 247 through 252
    Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324
      removed outlier: 3.995A  pdb=" N   TRP B 301 " --> pdb=" O   TYR B 562 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   SER B 305 " --> pdb=" O   ASN B 558 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   ASN B 558 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 334 through 340
      removed outlier: 3.706A  pdb=" N   GLY B 336 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ILE B 354 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 378 through 384
      removed outlier: 3.863A  pdb=" N   SER B 380 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 423 through 426
      removed outlier: 6.561A  pdb=" N   ILE B 440 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470
      removed outlier: 6.600A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 510 through 514
      removed outlier: 5.592A  pdb=" N   PHE B 518 " --> pdb=" O   GLU B 529 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   VAL B 526 " --> pdb=" O   TYR B 542 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 576 through 582
      removed outlier: 5.740A  pdb=" N   LEU B 577 " --> pdb=" O   SER B 592 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   SER B 592 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 623 through 629
      removed outlier: 6.553A  pdb=" N   GLU B 623 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   SER B 616 " --> pdb=" O   GLU B 623 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   VAL B 625 " --> pdb=" O   VAL B 614 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B 614 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   SER B 627 " --> pdb=" O   VAL B 612 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B 612 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 623 through 629
      removed outlier: 6.553A  pdb=" N   GLU B 623 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   SER B 616 " --> pdb=" O   GLU B 623 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   VAL B 625 " --> pdb=" O   VAL B 614 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B 614 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   SER B 627 " --> pdb=" O   VAL B 612 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B 612 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 698 through 701
      removed outlier: 5.849A  pdb=" N   PHE B 699 " --> pdb=" O   LYS B 688 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LYS B 688 " --> pdb=" O   PHE B 699 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR B 701 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA B 926 " --> pdb=" O   VAL B 681 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 710 through 712
      removed outlier: 3.920A  pdb=" N   SER B 741 " --> pdb=" O   THR B 728 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 790 through 796
      removed outlier: 4.010A  pdb=" N   THR B 809 " --> pdb=" O   THR B 806 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   VAL B 810 " --> pdb=" O   LEU B 823 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 832 through 840
      removed outlier: 5.768A  pdb=" N   VAL B 834 " --> pdb=" O   GLN B 851 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   GLN B 851 " --> pdb=" O   VAL B 834 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   GLY B 836 " --> pdb=" O   LEU B 849 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU B 858 " --> pdb=" O   ALA B 878 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   ALA B 878 " --> pdb=" O   LEU B 858 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   ARG B 860 " --> pdb=" O   ILE B 876 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ILE B 876 " --> pdb=" O   ARG B 860 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   SER B 862 " --> pdb=" O   THR B 874 " (cutoff:3.500A)
      removed outlier: 9.568A  pdb=" N   THR B 874 " --> pdb=" O   SER B 862 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 884 through 891
      removed outlier: 6.728A  pdb=" N   ALA B 888 " --> pdb=" O   ILE B 899 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ILE B 899 " --> pdb=" O   ALA B 888 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 958 through 961
    Processing sheet with id=AC4, first strand: chain 'B' and resid 982 through 983
    Processing sheet with id=AC5, first strand: chain 'B' and resid 1021 through 1026

    297 hydrogen bonds defined for protein.
    756 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: 4.22

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7677
        1.03 -     1.23: 44
        1.23 -     1.43: 3731
        1.43 -     1.62: 4663
        1.62 -     1.82: 49
  Bond restraints: 16164
  Sorted by residual:
  bond pdb=" N   CYS B  24 "
       pdb=" CA  CYS B  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.05e+00
  bond pdb=" N   CYS B  24 "
       pdb=" H   CYS B  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C   ILE B 412 "
       pdb=" O   ILE B 412 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.19e-02 7.06e+03 9.29e-01
  bond pdb=" C   ARG B 750 "
       pdb=" O   ARG B 750 "
    ideal  model  delta    sigma   weight residual
    1.234  1.247 -0.012 1.30e-02 5.92e+03 9.00e-01
  bond pdb=" CA  VAL B 881 "
       pdb=" CB  VAL B 881 "
    ideal  model  delta    sigma   weight residual
    1.528  1.539 -0.011 1.34e-02 5.57e+03 7.21e-01
  ... (remaining 16159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 26616
        0.91 -     1.82: 2203
        1.82 -     2.73: 107
        2.73 -     3.64: 48
        3.64 -     4.54: 7
  Bond angle restraints: 28981
  Sorted by residual:
  angle pdb=" N   ARG B 750 "
        pdb=" CA  ARG B 750 "
        pdb=" C   ARG B 750 "
      ideal   model   delta    sigma   weight residual
     112.13  108.03    4.10 1.37e+00 5.33e-01 8.97e+00
  angle pdb=" N   SER B  25 "
        pdb=" CA  SER B  25 "
        pdb=" CB  SER B  25 "
      ideal   model   delta    sigma   weight residual
     114.17  111.06    3.11 1.14e+00 7.69e-01 7.46e+00
  angle pdb=" C   SER B 919 "
        pdb=" N   GLU B 920 "
        pdb=" CA  GLU B 920 "
      ideal   model   delta    sigma   weight residual
     120.09  123.30   -3.21 1.25e+00 6.40e-01 6.61e+00
  angle pdb=" N   GLU B 866 "
        pdb=" CA  GLU B 866 "
        pdb=" C   GLU B 866 "
      ideal   model   delta    sigma   weight residual
     113.88  110.96    2.92 1.23e+00 6.61e-01 5.62e+00
  angle pdb=" N   SER B 200 "
        pdb=" CA  SER B 200 "
        pdb=" C   SER B 200 "
      ideal   model   delta    sigma   weight residual
     107.93  111.83   -3.90 1.65e+00 3.67e-01 5.58e+00
  ... (remaining 28976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 7546
       16.86 -    33.72: 296
       33.72 -    50.57: 91
       50.57 -    67.43: 39
       67.43 -    84.29: 11
  Dihedral angle restraints: 7983
    sinusoidal: 4297
      harmonic: 3686
  Sorted by residual:
  dihedral pdb=" CB  CYS B  72 "
           pdb=" SG  CYS B  72 "
           pdb=" SG  CYS B  93 "
           pdb=" CB  CYS B  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.95  -34.95     1      1.00e+01 1.00e-02 1.73e+01
  dihedral pdb=" CA  TRP B 608 "
           pdb=" C   TRP B 608 "
           pdb=" N   THR B 609 "
           pdb=" CA  THR B 609 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.76   18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  VAL B 743 "
           pdb=" C   VAL B 743 "
           pdb=" N   PRO B 744 "
           pdb=" CA  PRO B 744 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.73  -17.27     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 7980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 807
       0.029 -    0.058: 330
       0.058 -    0.087: 49
       0.087 -    0.116: 96
       0.116 -    0.146: 24
  Chirality restraints: 1306
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN B 480 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  VAL B1008 "
            pdb=" N   VAL B1008 "
            pdb=" C   VAL B1008 "
            pdb=" CB  VAL B1008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" C1  NAG B2401 "
            pdb=" ND2 ASN B 123 "
            pdb=" C2  NAG B2401 "
            pdb=" O5  NAG B2401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 1303 not shown)

  Planarity restraints: 2418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 282 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 283 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 283 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 283 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 653 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.65e+00
        pdb=" N   PRO B 654 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 654 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 654 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 574 "    0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO B 575 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 575 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 575 "    0.017 5.00e-02 4.00e+02
  ... (remaining 2415 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 9063
        2.45 -     2.99: 34785
        2.99 -     3.52: 40156
        3.52 -     4.06: 57670
        4.06 -     4.60: 81099
  Nonbonded interactions: 222773
  Sorted by model distance:
  nonbonded pdb=" H   THR B 171 "
            pdb=" HG1 THR B 197 "
     model   vdw
     1.908 2.100
  nonbonded pdb=" H   THR B 643 "
            pdb=" HG1 THR B 668 "
     model   vdw
     1.909 2.100
  nonbonded pdb=" HG1 THR B 806 "
            pdb=" H   THR B 809 "
     model   vdw
     1.911 2.100
  nonbonded pdb=" H   THR B 668 "
            pdb=" HG1 THR B 668 "
     model   vdw
     1.932 2.100
  nonbonded pdb=" H   THR B 632 "
            pdb=" HG1 THR B 632 "
     model   vdw
     1.939 2.100
  ... (remaining 222768 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.900
  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:             0.090
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.400
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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      :  0.002   0.033   8509  Z= 0.125
  Angle     :  0.536   4.252  11639  Z= 0.314
  Chirality :  0.043   0.146   1306
  Planarity :  0.003   0.032   1454
  Dihedral  :  9.232  84.288   3223
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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: -0.52 (0.27), residues: 997
  helix:  3.39 (0.75), residues: 60
  sheet: -0.87 (0.25), residues: 393
  loop : -0.25 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 895 
 TYR   0.007   0.001   TYR B 701 
 PHE   0.007   0.001   PHE B 490 
 TRP   0.008   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8484)
  covalent geometry    : angle       0.52562 (11574)
  SS BOND              : bond        0.00128 (   10)
  SS BOND              : angle       0.73587 (   20)
  hydrogen bonds       : bond        0.19872 (  277)
  hydrogen bonds       : angle       9.23067 (  756)
  link_BETA1-4         : bond        0.00339 (    1)
  link_BETA1-4         : angle       1.78066 (    3)
  link_NAG-ASN         : bond        0.00270 (   14)
  link_NAG-ASN         : angle       1.68790 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7801 (mp0)
REVERT: B  301 TRP cc_start: 0.8344 (m100) cc_final: 0.8084 (m100)
REVERT: B  460 LYS cc_start: 0.9250 (tttt) cc_final: 0.9031 (tttm)
REVERT: B  484 GLN cc_start: 0.8388 (mt0) cc_final: 0.7774 (tt0)
REVERT: B  505 LEU cc_start: 0.8968 (mp) cc_final: 0.8768 (mt)
REVERT: B  515 ASP cc_start: 0.8553 (t0) cc_final: 0.8258 (t0)
REVERT: B  516 ASN cc_start: 0.8823 (m-40) cc_final: 0.8363 (t0)
REVERT: B  747 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8855 (mtpp)
REVERT: B  871 ILE cc_start: 0.8786 (mm) cc_final: 0.8581 (pp)
REVERT: B 1019 PHE cc_start: 0.7832 (t80) cc_final: 0.7568 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 1.4520
  time to fit residues: 102.8438
Evaluate side-chains
  46 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.092201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.065924 restraints weight = 40096.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.50
r_work: 0.2732 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8509  Z= 0.182
  Angle     :  0.521   5.542  11639  Z= 0.273
  Chirality :  0.044   0.144   1306
  Planarity :  0.004   0.034   1454
  Dihedral  :  4.443  28.772   1400
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.81 %
    Favored  : 95.96 %
  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: -0.42 (0.27), residues: 997
  helix:  3.36 (0.74), residues: 60
  sheet: -0.75 (0.24), residues: 402
  loop : -0.19 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 901 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.011   0.001   PHE B 225 
 TRP   0.010   0.001   TRP B 848 
 HIS   0.005   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 8484)
  covalent geometry    : angle       0.51057 (11574)
  SS BOND              : bond        0.00390 (   10)
  SS BOND              : angle       0.79921 (   20)
  hydrogen bonds       : bond        0.04694 (  277)
  hydrogen bonds       : angle       6.64729 (  756)
  link_BETA1-4         : bond        0.00231 (    1)
  link_BETA1-4         : angle       1.72293 (    3)
  link_NAG-ASN         : bond        0.00210 (   14)
  link_NAG-ASN         : angle       1.67297 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7879 (mp0)
REVERT: B  301 TRP cc_start: 0.8515 (m100) cc_final: 0.8302 (m100)
REVERT: B  484 GLN cc_start: 0.8443 (mt0) cc_final: 0.7992 (tt0)
REVERT: B  515 ASP cc_start: 0.8471 (t0) cc_final: 0.8213 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8941 (m-40) cc_final: 0.8608 (t0)
REVERT: B 1019 PHE cc_start: 0.7928 (t80) cc_final: 0.7033 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 49
  average time/residue: 1.4052
  time to fit residues: 73.2661
Evaluate side-chains
  42 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.091816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.065292 restraints weight = 40773.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.51
r_work: 0.2709 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8509  Z= 0.169
  Angle     :  0.506   6.483  11639  Z= 0.262
  Chirality :  0.045   0.159   1306
  Planarity :  0.003   0.033   1454
  Dihedral  :  4.484  31.492   1400
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.37 %
    Favored  : 95.18 %
  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: -0.44 (0.27), residues: 997
  helix:  3.41 (0.74), residues: 60
  sheet: -0.70 (0.24), residues: 411
  loop : -0.26 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 901 
 TYR   0.009   0.001   TYR B 342 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8484)
  covalent geometry    : angle       0.49696 (11574)
  SS BOND              : bond        0.00201 (   10)
  SS BOND              : angle       0.71546 (   20)
  hydrogen bonds       : bond        0.04066 (  277)
  hydrogen bonds       : angle       6.09294 (  756)
  link_BETA1-4         : bond        0.00077 (    1)
  link_BETA1-4         : angle       1.55566 (    3)
  link_NAG-ASN         : bond        0.00224 (   14)
  link_NAG-ASN         : angle       1.59357 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7977 (mp0)
REVERT: B  484 GLN cc_start: 0.8433 (mt0) cc_final: 0.7947 (tt0)
REVERT: B  515 ASP cc_start: 0.8498 (t0) cc_final: 0.8219 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8896 (m-40) cc_final: 0.8504 (t0)
REVERT: B  883 GLU cc_start: 0.8686 (mp0) cc_final: 0.8349 (mp0)
REVERT: B 1019 PHE cc_start: 0.7928 (t80) cc_final: 0.7044 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 43
  average time/residue: 1.3753
  time to fit residues: 63.0002
Evaluate side-chains
  43 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 68 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.091959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.065562 restraints weight = 40167.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.50
r_work: 0.2716 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2569 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8509  Z= 0.152
  Angle     :  0.492   4.914  11639  Z= 0.255
  Chirality :  0.044   0.162   1306
  Planarity :  0.003   0.054   1454
  Dihedral  :  4.456  31.944   1400
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.48 %
    Favored  : 95.07 %
  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: -0.41 (0.27), residues: 997
  helix:  3.47 (0.73), residues: 60
  sheet: -0.69 (0.24), residues: 412
  loop : -0.25 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 253 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8484)
  covalent geometry    : angle       0.48276 (11574)
  SS BOND              : bond        0.00155 (   10)
  SS BOND              : angle       0.61537 (   20)
  hydrogen bonds       : bond        0.03696 (  277)
  hydrogen bonds       : angle       5.80716 (  756)
  link_BETA1-4         : bond        0.00150 (    1)
  link_BETA1-4         : angle       1.48176 (    3)
  link_NAG-ASN         : bond        0.00197 (   14)
  link_NAG-ASN         : angle       1.54977 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7972 (mp0)
REVERT: B  484 GLN cc_start: 0.8438 (mt0) cc_final: 0.7956 (tt0)
REVERT: B  515 ASP cc_start: 0.8486 (t0) cc_final: 0.8202 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8963 (m-40) cc_final: 0.8507 (t0)
REVERT: B  665 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8516 (ttp80)
REVERT: B  883 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8342 (mp0)
REVERT: B 1019 PHE cc_start: 0.7930 (t80) cc_final: 0.7028 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 1.5639
  time to fit residues: 74.5264
Evaluate side-chains
  42 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  823 LEU
Chi-restraints excluded: chain B residue  883 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.092283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.066117 restraints weight = 40529.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.48
r_work: 0.2727 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8509  Z= 0.126
  Angle     :  0.478   4.668  11639  Z= 0.247
  Chirality :  0.044   0.163   1306
  Planarity :  0.003   0.055   1454
  Dihedral  :  4.372  31.145   1400
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  4.60 %
    Favored  : 94.73 %
  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: -0.36 (0.27), residues: 997
  helix:  3.57 (0.74), residues: 60
  sheet: -0.65 (0.24), residues: 412
  loop : -0.22 (0.29), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 901 
 TYR   0.009   0.001   TYR B 771 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8484)
  covalent geometry    : angle       0.47015 (11574)
  SS BOND              : bond        0.00141 (   10)
  SS BOND              : angle       0.55032 (   20)
  hydrogen bonds       : bond        0.03478 (  277)
  hydrogen bonds       : angle       5.63488 (  756)
  link_BETA1-4         : bond        0.00099 (    1)
  link_BETA1-4         : angle       1.41149 (    3)
  link_NAG-ASN         : bond        0.00170 (   14)
  link_NAG-ASN         : angle       1.47563 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7955 (mp0)
REVERT: B  484 GLN cc_start: 0.8437 (mt0) cc_final: 0.7951 (tt0)
REVERT: B  515 ASP cc_start: 0.8480 (t0) cc_final: 0.8186 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8973 (m-40) cc_final: 0.8509 (t0)
REVERT: B  883 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8343 (mp0)
REVERT: B 1019 PHE cc_start: 0.7920 (t80) cc_final: 0.7025 (m-80)
  outliers start: 6
  outliers final: 2
  residues processed: 44
  average time/residue: 1.2379
  time to fit residues: 58.3605
Evaluate side-chains
  42 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  883 GLU
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.092089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.065883 restraints weight = 40210.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.48
r_work: 0.2721 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8509  Z= 0.145
  Angle     :  0.481   4.676  11639  Z= 0.248
  Chirality :  0.044   0.162   1306
  Planarity :  0.003   0.033   1454
  Dihedral  :  4.355  32.218   1400
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.82 %
    Favored  : 94.62 %
  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: -0.37 (0.27), residues: 997
  helix:  3.60 (0.73), residues: 60
  sheet: -0.62 (0.24), residues: 417
  loop : -0.26 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 901 
 TYR   0.010   0.001   TYR B 416 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8484)
  covalent geometry    : angle       0.47250 (11574)
  SS BOND              : bond        0.00128 (   10)
  SS BOND              : angle       0.55301 (   20)
  hydrogen bonds       : bond        0.03443 (  277)
  hydrogen bonds       : angle       5.52658 (  756)
  link_BETA1-4         : bond        0.00091 (    1)
  link_BETA1-4         : angle       1.43584 (    3)
  link_NAG-ASN         : bond        0.00190 (   14)
  link_NAG-ASN         : angle       1.48603 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8000 (mp0)
REVERT: B  484 GLN cc_start: 0.8423 (mt0) cc_final: 0.7958 (tt0)
REVERT: B  515 ASP cc_start: 0.8472 (t0) cc_final: 0.8176 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8977 (m-40) cc_final: 0.8495 (t0)
REVERT: B  871 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8129 (pp)
REVERT: B  883 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8353 (mp0)
REVERT: B 1019 PHE cc_start: 0.7956 (t80) cc_final: 0.7066 (m-80)
  outliers start: 5
  outliers final: 2
  residues processed: 42
  average time/residue: 1.1707
  time to fit residues: 52.9836
Evaluate side-chains
  43 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  871 ILE
Chi-restraints excluded: chain B residue  883 GLU
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.091985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.065840 restraints weight = 40361.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.48
r_work: 0.2721 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2574 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8509  Z= 0.146
  Angle     :  0.482   4.649  11639  Z= 0.249
  Chirality :  0.044   0.162   1306
  Planarity :  0.004   0.071   1454
  Dihedral  :  4.365  33.187   1400
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.16 %
    Favored  : 94.28 %
  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: -0.36 (0.27), residues: 997
  helix:  3.60 (0.73), residues: 60
  sheet: -0.63 (0.24), residues: 419
  loop : -0.24 (0.29), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 253 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8484)
  covalent geometry    : angle       0.47453 (11574)
  SS BOND              : bond        0.00132 (   10)
  SS BOND              : angle       0.52780 (   20)
  hydrogen bonds       : bond        0.03421 (  277)
  hydrogen bonds       : angle       5.47808 (  756)
  link_BETA1-4         : bond        0.00146 (    1)
  link_BETA1-4         : angle       1.40973 (    3)
  link_NAG-ASN         : bond        0.00190 (   14)
  link_NAG-ASN         : angle       1.46841 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7963 (mp0)
REVERT: B  484 GLN cc_start: 0.8424 (mt0) cc_final: 0.7959 (tt0)
REVERT: B  515 ASP cc_start: 0.8538 (t0) cc_final: 0.8239 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8980 (m-40) cc_final: 0.8491 (t0)
REVERT: B  883 GLU cc_start: 0.8715 (mp0) cc_final: 0.8321 (mp0)
REVERT: B 1019 PHE cc_start: 0.7947 (t80) cc_final: 0.7066 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 43
  average time/residue: 1.1591
  time to fit residues: 53.6967
Evaluate side-chains
  41 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  823 LEU
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0170
   chunk 60 optimal weight:    0.3980
   chunk 64 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0020
   chunk 93 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.3426

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.092812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.066395 restraints weight = 40345.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.52
r_work: 0.2739 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8509  Z= 0.092
  Angle     :  0.458   4.578  11639  Z= 0.237
  Chirality :  0.044   0.158   1306
  Planarity :  0.003   0.030   1454
  Dihedral  :  4.193  29.782   1400
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.38 %
    Favored  : 94.06 %
  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: -0.29 (0.27), residues: 997
  helix:  3.68 (0.73), residues: 60
  sheet: -0.59 (0.24), residues: 412
  loop : -0.20 (0.29), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 901 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.010   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8484)
  covalent geometry    : angle       0.45183 (11574)
  SS BOND              : bond        0.00115 (   10)
  SS BOND              : angle       0.47412 (   20)
  hydrogen bonds       : bond        0.03102 (  277)
  hydrogen bonds       : angle       5.35251 (  756)
  link_BETA1-4         : bond        0.00154 (    1)
  link_BETA1-4         : angle       1.32298 (    3)
  link_NAG-ASN         : bond        0.00154 (   14)
  link_NAG-ASN         : angle       1.31782 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: B  484 GLN cc_start: 0.8358 (mt0) cc_final: 0.7859 (tt0)
REVERT: B  515 ASP cc_start: 0.8529 (t0) cc_final: 0.8229 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8980 (m-40) cc_final: 0.8486 (t0)
REVERT: B  883 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8341 (mp0)
REVERT: B 1019 PHE cc_start: 0.7983 (t80) cc_final: 0.7136 (m-80)
  outliers start: 5
  outliers final: 2
  residues processed: 42
  average time/residue: 1.1527
  time to fit residues: 52.1904
Evaluate side-chains
  40 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  883 GLU
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0970
   chunk 57 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.092465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.066027 restraints weight = 40058.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.52
r_work: 0.2728 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8509  Z= 0.125
  Angle     :  0.468   4.516  11639  Z= 0.241
  Chirality :  0.044   0.160   1306
  Planarity :  0.004   0.077   1454
  Dihedral  :  4.194  30.691   1400
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.61 %
    Favored  : 93.95 %
  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: -0.28 (0.27), residues: 997
  helix:  3.64 (0.72), residues: 60
  sheet: -0.55 (0.24), residues: 419
  loop : -0.20 (0.29), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 253 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8484)
  covalent geometry    : angle       0.46153 (11574)
  SS BOND              : bond        0.00117 (   10)
  SS BOND              : angle       0.49284 (   20)
  hydrogen bonds       : bond        0.03196 (  277)
  hydrogen bonds       : angle       5.30362 (  756)
  link_BETA1-4         : bond        0.00123 (    1)
  link_BETA1-4         : angle       1.40107 (    3)
  link_NAG-ASN         : bond        0.00169 (   14)
  link_NAG-ASN         : angle       1.36471 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: B  515 ASP cc_start: 0.8508 (t0) cc_final: 0.8207 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8969 (m-40) cc_final: 0.8648 (t0)
REVERT: B  871 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8196 (pp)
REVERT: B  883 GLU cc_start: 0.8689 (mp0) cc_final: 0.8329 (mp0)
REVERT: B 1019 PHE cc_start: 0.7924 (t80) cc_final: 0.7638 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 41
  average time/residue: 1.0614
  time to fit residues: 47.1026
Evaluate side-chains
  40 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  823 LEU
Chi-restraints excluded: chain B residue  871 ILE
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.091981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.065709 restraints weight = 40465.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.49
r_work: 0.2718 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2573 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8509  Z= 0.171
  Angle     :  0.486   4.649  11639  Z= 0.251
  Chirality :  0.044   0.161   1306
  Planarity :  0.003   0.033   1454
  Dihedral  :  4.307  33.880   1400
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.61 %
    Favored  : 93.95 %
  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: -0.33 (0.27), residues: 997
  helix:  3.57 (0.72), residues: 60
  sheet: -0.56 (0.24), residues: 418
  loop : -0.26 (0.29), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 901 
 TYR   0.011   0.001   TYR B 416 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8484)
  covalent geometry    : angle       0.47803 (11574)
  SS BOND              : bond        0.00128 (   10)
  SS BOND              : angle       0.54056 (   20)
  hydrogen bonds       : bond        0.03395 (  277)
  hydrogen bonds       : angle       5.33038 (  756)
  link_BETA1-4         : bond        0.00097 (    1)
  link_BETA1-4         : angle       1.41783 (    3)
  link_NAG-ASN         : bond        0.00221 (   14)
  link_NAG-ASN         : angle       1.44575 (   42)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B  515 ASP cc_start: 0.8532 (t0) cc_final: 0.8226 (OUTLIER)
REVERT: B  516 ASN cc_start: 0.8989 (m-40) cc_final: 0.8558 (t0)
REVERT: B  883 GLU cc_start: 0.8709 (mp0) cc_final: 0.8304 (mp0)
REVERT: B 1019 PHE cc_start: 0.7930 (t80) cc_final: 0.7630 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 1.1250
  time to fit residues: 48.5024
Evaluate side-chains
  39 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  823 LEU
Chi-restraints excluded: chain B residue 1021 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0970
   chunk 74 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0570
   chunk 56 optimal weight:    0.0170
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.1612

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.093272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.067038 restraints weight = 40151.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.51
r_work: 0.2748 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8509  Z= 0.079
  Angle     :  0.455   4.522  11639  Z= 0.234
  Chirality :  0.044   0.157   1306
  Planarity :  0.003   0.062   1454
  Dihedral  :  4.098  28.410   1400
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.61 %
    Favored  : 93.95 %
  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: -0.22 (0.27), residues: 997
  helix:  3.72 (0.73), residues: 60
  sheet: -0.49 (0.25), residues: 407
  loop : -0.20 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 253 
 TYR   0.010   0.001   TYR B 771 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.000   HIS B 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00172 ( 8484)
  covalent geometry    : angle       0.44887 (11574)
  SS BOND              : bond        0.00123 (   10)
  SS BOND              : angle       0.45650 (   20)
  hydrogen bonds       : bond        0.02934 (  277)
  hydrogen bonds       : angle       5.20297 (  756)
  link_BETA1-4         : bond        0.00306 (    1)
  link_BETA1-4         : angle       1.28132 (    3)
  link_NAG-ASN         : bond        0.00180 (   14)
  link_NAG-ASN         : angle       1.22994 (   42)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4853.59 seconds
wall clock time: 82 minutes 45.63 seconds (4965.63 seconds total)