Starting phenix.real_space_refine
on Wed Mar  4 00:05:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty4_26165/03_2026/7ty4_26165.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.043
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
     P       2      5.49       5
     S      36      5.16       5
     C    5798      2.51       5
     N    1310      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 8636
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    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: "D"
      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: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 187
          Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 187
          Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 37
          Classifications: {'water': 37}
          Link IDs: {None: 36}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 35
          Classifications: {'water': 35}
          Link IDs: {None: 34}
  Time building chain proxies: 1.85, per 1000 atoms: 0.21
  Number of scatterers: 8636
  At special positions: 0
  Unit cell: (112.98, 97.916, 83.928, 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
     P       2     15.00
     O    1490      8.00
     N    1310      7.00
     C    5798      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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-ASN
      " NAG C   1 " - " ASN A 642 "
      " NAG D   1 " - " ASN B 642 "
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 222.7 milliseconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      74.6% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 392 through 399
    Processing helix  chain 'A' and resid 402 through 432
      removed outlier: 3.501A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
      removed outlier: 3.626A  pdb=" N   GLY A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 3.859A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.511A  pdb=" N   LEU A 540 " --> pdb=" O   THR A 536 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE A 543 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
    Processing helix  chain 'A' and resid 598 through 608
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.509A  pdb=" N   MET A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 646
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 4.022A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
    Processing helix  chain 'A' and resid 701 through 719
      removed outlier: 3.756A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 738
    Processing helix  chain 'A' and resid 760 through 773
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.722A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 812
      removed outlier: 3.535A  pdb=" N   LEU A 811 " --> pdb=" O   ASP A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.824A  pdb=" N   HIS A 819 " --> pdb=" O   PRO A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
    Processing helix  chain 'A' and resid 829 through 853
    Processing helix  chain 'A' and resid 858 through 865
      removed outlier: 3.605A  pdb=" N   LEU A 865 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 872
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.606A  pdb=" N   ILE A 877 " --> pdb=" O   LEU A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 887
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 392 through 399
    Processing helix  chain 'B' and resid 402 through 432
      removed outlier: 3.501A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.626A  pdb=" N   GLY B 424 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 3.859A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 515
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.509A  pdb=" N   LEU B 540 " --> pdb=" O   THR B 536 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE B 543 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
    Processing helix  chain 'B' and resid 598 through 608
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 3.509A  pdb=" N   MET B 617 " --> pdb=" O   SER B 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 646
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 4.023A  pdb=" N   MET B 664 " --> pdb=" O   PRO B 660 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE B 665 " --> pdb=" O   ILE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 690
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 3.757A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 738
    Processing helix  chain 'B' and resid 760 through 773
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.724A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 812
      removed outlier: 3.534A  pdb=" N   LEU B 811 " --> pdb=" O   ASP B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 819
      removed outlier: 3.824A  pdb=" N   HIS B 819 " --> pdb=" O   PRO B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 827
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 858 through 865
      removed outlier: 3.605A  pdb=" N   LEU B 865 " --> pdb=" O   PHE B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 872
    Processing helix  chain 'B' and resid 873 through 878
      removed outlier: 3.607A  pdb=" N   ILE B 877 " --> pdb=" O   LEU B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463
      removed outlier: 4.792A  pdb=" N   VAL A 461 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742
      removed outlier: 7.659A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN A 754 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 752 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 461 through 463
      removed outlier: 4.792A  pdb=" N   VAL B 461 " --> pdb=" O   THR B 727 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742
      removed outlier: 7.661A  pdb=" N   VAL B 740 " --> pdb=" O   GLN B 754 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN B 754 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN B 752 " --> pdb=" O   GLY B 742 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1518 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: 1.40

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1254
        1.32 -     1.45: 2267
        1.45 -     1.57: 5201
        1.57 -     1.69: 4
        1.69 -     1.82: 66
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" N   LEU B 669 "
       pdb=" CA  LEU B 669 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.027 6.90e-03 2.10e+04 1.58e+01
  bond pdb=" N   LEU A 669 "
       pdb=" CA  LEU A 669 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.027 6.90e-03 2.10e+04 1.57e+01
  bond pdb=" N   LEU B 874 "
       pdb=" CA  LEU B 874 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 8.50e-03 1.38e+04 1.53e+01
  bond pdb=" N   THR A 431 "
       pdb=" CA  THR A 431 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.045 1.16e-02 7.43e+03 1.49e+01
  bond pdb=" N   THR B 431 "
       pdb=" CA  THR B 431 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.045 1.16e-02 7.43e+03 1.49e+01
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 9035
        2.13 -     4.26: 2548
        4.26 -     6.39: 383
        6.39 -     8.53: 6
        8.53 -    10.66: 2
  Bond angle restraints: 11974
  Sorted by residual:
  angle pdb=" N   VAL A 825 "
        pdb=" CA  VAL A 825 "
        pdb=" C   VAL A 825 "
      ideal   model   delta    sigma   weight residual
     111.00  105.19    5.81 1.09e+00 8.42e-01 2.84e+01
  angle pdb=" C   PRO B 598 "
        pdb=" N   GLY B 599 "
        pdb=" CA  GLY B 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.79   -5.76 1.12e+00 7.97e-01 2.65e+01
  angle pdb=" C   PRO A 598 "
        pdb=" N   GLY A 599 "
        pdb=" CA  GLY A 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.76   -5.73 1.12e+00 7.97e-01 2.62e+01
  angle pdb=" N   TYR B 596 "
        pdb=" CA  TYR B 596 "
        pdb=" C   TYR B 596 "
      ideal   model   delta    sigma   weight residual
     108.41  116.71   -8.30 1.63e+00 3.76e-01 2.59e+01
  angle pdb=" N   GLU A 429 "
        pdb=" CA  GLU A 429 "
        pdb=" C   GLU A 429 "
      ideal   model   delta    sigma   weight residual
     111.82  106.03    5.79 1.16e+00 7.43e-01 2.49e+01
  ... (remaining 11969 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.46: 5185
       19.46 -    38.93: 348
       38.93 -    58.39: 94
       58.39 -    77.85: 22
       77.85 -    97.32: 5
  Dihedral angle restraints: 5654
    sinusoidal: 2684
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" CA  TYR A 596 "
           pdb=" C   TYR A 596 "
           pdb=" N   PHE A 597 "
           pdb=" CA  PHE A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  TYR B 555 "
           pdb=" C   TYR B 555 "
           pdb=" N   ASN B 556 "
           pdb=" CA  ASN B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.45   19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TYR A 555 "
           pdb=" C   TYR A 555 "
           pdb=" N   ASN A 556 "
           pdb=" CA  ASN A 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.86   19.14     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 775
       0.077 -    0.154: 596
       0.154 -    0.232: 61
       0.232 -    0.309: 0
       0.309 -    0.386: 2
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-02 2.50e+03 6.67e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.29e+01
  chirality pdb=" CA  VAL A 825 "
            pdb=" N   VAL A 825 "
            pdb=" C   VAL A 825 "
            pdb=" CB  VAL A 825 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.83   -0.39 2.00e-01 2.50e+01 3.72e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1410
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.326 2.00e-02 2.50e+03   2.77e-01 9.58e+02
        pdb=" C7  NAG C   1 "   -0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.483 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.291 2.00e-02 2.50e+03   2.44e-01 7.44e+02
        pdb=" C7  NAG D   1 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.415 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "   -0.221 2.00e-02 2.50e+03   1.83e-01 4.17e+02
        pdb=" C7  NAG C   2 "    0.059 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "   -0.157 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "    0.299 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1407 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 401
        2.75 -     3.29: 9297
        3.29 -     3.83: 13893
        3.83 -     4.36: 18726
        4.36 -     4.90: 30644
  Nonbonded interactions: 72961
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 555 "
            pdb=" OH  TYR B 555 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASP B 607 "
            pdb=" O   HOH B2301 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE1 GLN A 447 "
            pdb=" O   HOH A2301 "
     model   vdw
     2.422 3.040
  nonbonded pdb=" OE1 GLN B 447 "
            pdb=" O   HOH B2302 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" NH2 ARG A 490 "
            pdb=" O   MET A 721 "
     model   vdw
     2.450 3.120
  ... (remaining 72956 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             2.420
  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:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.510
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:5.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
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      :  0.013   0.051   8796  Z= 0.998
  Angle     :  1.798  10.657  11986  Z= 1.370
  Chirality :  0.087   0.386   1434
  Planarity :  0.012   0.277   1408
  Dihedral  : 14.464  97.319   3738
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.87 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.47 %
    Favored  : 94.08 %
  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: -2.69 (0.22), residues: 1022
  helix: -1.56 (0.16), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.93 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 730 
 TYR   0.013   0.002   TYR B 628 
 PHE   0.016   0.002   PHE B 451 
 TRP   0.018   0.002   TRP A 492 
 HIS   0.005   0.002   HIS A 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.01305 ( 8792)
  covalent geometry    : angle       1.79787 (11974)
  hydrogen bonds       : bond        0.23428 (  524)
  hydrogen bonds       : angle       8.20359 ( 1518)
  link_BETA1-4         : bond        0.00201 (    2)
  link_BETA1-4         : angle       0.66710 (    6)
  link_NAG-ASN         : bond        0.00180 (    2)
  link_NAG-ASN         : angle       2.55403 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 ASN cc_start: 0.8611 (m-40) cc_final: 0.8260 (m110)
REVERT: A  498 ILE cc_start: 0.9632 (mt) cc_final: 0.9415 (mp)
REVERT: A  681 GLU cc_start: 0.8803 (tt0) cc_final: 0.8347 (tt0)
REVERT: A  741 MET cc_start: 0.9316 (mmm) cc_final: 0.8973 (mmm)
REVERT: A  880 ASN cc_start: 0.9250 (p0) cc_final: 0.9047 (t0)
REVERT: B  433 ASN cc_start: 0.9395 (m-40) cc_final: 0.9174 (m-40)
REVERT: B  482 ASN cc_start: 0.8615 (m-40) cc_final: 0.8244 (m110)
REVERT: B  498 ILE cc_start: 0.9630 (mt) cc_final: 0.9424 (mp)
REVERT: B  681 GLU cc_start: 0.8808 (tt0) cc_final: 0.8352 (tt0)
REVERT: B  741 MET cc_start: 0.9318 (mmm) cc_final: 0.8975 (mmm)
REVERT: B  880 ASN cc_start: 0.9252 (p0) cc_final: 0.9038 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 130
  average time/residue: 0.4334
  time to fit residues: 61.0883
Evaluate side-chains
  73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain B residue  511 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 433 ASN
A 457 GLN
A 545 GLN
A 564 GLN
A 683 GLN
B 457 GLN
B 545 GLN
B 564 GLN
B 834 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.058890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.049630 restraints weight = 29075.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 3.27
r_work: 0.2649 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8796  Z= 0.164
  Angle     :  0.660   9.904  11986  Z= 0.314
  Chirality :  0.040   0.146   1434
  Planarity :  0.005   0.043   1408
  Dihedral  : 10.145  67.683   1840
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 10.16 %
    Favored  : 87.17 %
  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:  0.72 (0.25), residues: 1022
  helix:  1.32 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.32 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 603 
 TYR   0.008   0.001   TYR A 824 
 PHE   0.018   0.001   PHE A 411 
 TRP   0.028   0.003   TRP A 662 
 HIS   0.002   0.001   HIS B 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8792)
  covalent geometry    : angle       0.65840 (11974)
  hydrogen bonds       : bond        0.05056 (  524)
  hydrogen bonds       : angle       4.64746 ( 1518)
  link_BETA1-4         : bond        0.00401 (    2)
  link_BETA1-4         : angle       1.74842 (    6)
  link_NAG-ASN         : bond        0.00281 (    2)
  link_NAG-ASN         : angle       1.54429 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8798 (pp)
REVERT: A  498 ILE cc_start: 0.9301 (mt) cc_final: 0.9099 (mp)
REVERT: A  554 ASN cc_start: 0.8466 (t0) cc_final: 0.8134 (t0)
REVERT: A  681 GLU cc_start: 0.8941 (tt0) cc_final: 0.8164 (tm-30)
REVERT: A  696 MET cc_start: 0.8602 (mmm) cc_final: 0.8285 (mmm)
REVERT: A  721 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8783 (mtm)
REVERT: A  759 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8367 (pm20)
REVERT: B  386 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: B  554 ASN cc_start: 0.8391 (t0) cc_final: 0.7955 (t0)
REVERT: B  681 GLU cc_start: 0.8947 (tt0) cc_final: 0.8175 (tm-30)
REVERT: B  721 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8476 (mtp)
REVERT: B  759 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8471 (pm20)
  outliers start: 24
  outliers final: 0
  residues processed: 96
  average time/residue: 0.3935
  time to fit residues: 41.5797
Evaluate side-chains
  74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  759 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 683 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.057970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.048917 restraints weight = 29508.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 3.27
r_work: 0.2634 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8796  Z= 0.153
  Angle     :  0.603   7.734  11986  Z= 0.286
  Chirality :  0.039   0.140   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  9.550  62.215   1836
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.05 %
    Favored  : 86.16 %
  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 (0.26), residues: 1022
  helix:  1.91 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.97 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 603 
 TYR   0.012   0.001   TYR A 824 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.031   0.002   TRP A 662 
 HIS   0.002   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8792)
  covalent geometry    : angle       0.60126 (11974)
  hydrogen bonds       : bond        0.04202 (  524)
  hydrogen bonds       : angle       4.46836 ( 1518)
  link_BETA1-4         : bond        0.00323 (    2)
  link_BETA1-4         : angle       1.11003 (    6)
  link_NAG-ASN         : bond        0.00268 (    2)
  link_NAG-ASN         : angle       2.06551 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 ILE cc_start: 0.9294 (mt) cc_final: 0.9050 (mp)
REVERT: A  554 ASN cc_start: 0.8773 (t0) cc_final: 0.8384 (t0)
REVERT: A  681 GLU cc_start: 0.8901 (tt0) cc_final: 0.8156 (tm-30)
REVERT: A  696 MET cc_start: 0.8699 (mmm) cc_final: 0.8120 (mmm)
REVERT: A  721 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8357 (mpp)
REVERT: B  554 ASN cc_start: 0.8826 (t0) cc_final: 0.8336 (t0)
REVERT: B  681 GLU cc_start: 0.8933 (tt0) cc_final: 0.8176 (tm-30)
REVERT: B  721 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8712 (mmm)
  outliers start: 25
  outliers final: 3
  residues processed: 88
  average time/residue: 0.3941
  time to fit residues: 38.1592
Evaluate side-chains
  71 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  828 VAL
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3002 r_free = 0.3002 target = 0.056574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.047778 restraints weight = 30625.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2737 rms_B_bonded: 3.28
r_work: 0.2601 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8796  Z= 0.193
  Angle     :  0.604   7.352  11986  Z= 0.286
  Chirality :  0.040   0.135   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  9.332  59.828   1836
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.83 %
    Favored  : 85.83 %
  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:  1.73 (0.26), residues: 1022
  helix:  2.04 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.80 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 656 
 TYR   0.013   0.001   TYR A 824 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.017   0.002   TRP B 662 
 HIS   0.002   0.001   HIS B 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8792)
  covalent geometry    : angle       0.60167 (11974)
  hydrogen bonds       : bond        0.04062 (  524)
  hydrogen bonds       : angle       4.40518 ( 1518)
  link_BETA1-4         : bond        0.00139 (    2)
  link_BETA1-4         : angle       1.15992 (    6)
  link_NAG-ASN         : bond        0.00404 (    2)
  link_NAG-ASN         : angle       1.96526 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 ILE cc_start: 0.9299 (mt) cc_final: 0.9057 (mp)
REVERT: A  554 ASN cc_start: 0.8889 (t0) cc_final: 0.8454 (t0)
REVERT: A  664 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8961 (mtm)
REVERT: A  681 GLU cc_start: 0.8943 (tt0) cc_final: 0.8400 (tm-30)
REVERT: A  696 MET cc_start: 0.8786 (mmm) cc_final: 0.8104 (mmm)
REVERT: A  721 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8434 (mtp)
REVERT: A  759 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8361 (pm20)
REVERT: B  433 ASN cc_start: 0.9573 (m110) cc_final: 0.9324 (m110)
REVERT: B  554 ASN cc_start: 0.8896 (t0) cc_final: 0.8430 (t0)
REVERT: B  681 GLU cc_start: 0.8928 (tt0) cc_final: 0.8374 (tm-30)
REVERT: B  721 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8242 (mtp)
REVERT: B  759 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8559 (pm20)
  outliers start: 21
  outliers final: 8
  residues processed: 79
  average time/residue: 0.3924
  time to fit residues: 34.1479
Evaluate side-chains
  77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  828 VAL
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0030
   chunk 62 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0980
   overall best weight:    0.2990

-------------------------------------------------------------------------------
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 = 0.3048 r_free = 0.3048 target = 0.058417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.049679 restraints weight = 29797.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 3.28
r_work: 0.2658 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8796  Z= 0.108
  Angle     :  0.570   8.783  11986  Z= 0.266
  Chirality :  0.038   0.133   1434
  Planarity :  0.005   0.048   1408
  Dihedral  :  8.985  59.982   1836
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.39 %
    Favored  : 85.16 %
  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:  1.91 (0.27), residues: 1022
  helix:  2.14 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.62 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 656 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.014   0.001   PHE A 471 
 TRP   0.014   0.001   TRP B 662 
 HIS   0.002   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8792)
  covalent geometry    : angle       0.56788 (11974)
  hydrogen bonds       : bond        0.03610 (  524)
  hydrogen bonds       : angle       4.22992 ( 1518)
  link_BETA1-4         : bond        0.00279 (    2)
  link_BETA1-4         : angle       1.00714 (    6)
  link_NAG-ASN         : bond        0.00080 (    2)
  link_NAG-ASN         : angle       1.88726 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.8906 (t0) cc_final: 0.8476 (t0)
REVERT: A  681 GLU cc_start: 0.8916 (tt0) cc_final: 0.8213 (tt0)
REVERT: A  721 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8350 (mpp)
REVERT: A  759 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8242 (pm20)
REVERT: B  433 ASN cc_start: 0.9591 (m110) cc_final: 0.9268 (m110)
REVERT: B  554 ASN cc_start: 0.8977 (t0) cc_final: 0.8517 (t0)
REVERT: B  559 MET cc_start: 0.8788 (mtm) cc_final: 0.8400 (mtt)
REVERT: B  681 GLU cc_start: 0.8916 (tt0) cc_final: 0.8194 (tt0)
REVERT: B  721 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8258 (mmm)
REVERT: B  759 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8456 (pm20)
  outliers start: 22
  outliers final: 7
  residues processed: 93
  average time/residue: 0.3778
  time to fit residues: 38.7786
Evaluate side-chains
  77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.2998 r_free = 0.2998 target = 0.055875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.047164 restraints weight = 30461.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 3.26
r_work: 0.2602 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8796  Z= 0.204
  Angle     :  0.630   8.995  11986  Z= 0.292
  Chirality :  0.041   0.152   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.986  59.802   1836
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.17 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.27), residues: 1022
  helix:  2.19 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.54 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 656 
 TYR   0.013   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.013   0.001   TRP B 662 
 HIS   0.002   0.001   HIS B 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8792)
  covalent geometry    : angle       0.62790 (11974)
  hydrogen bonds       : bond        0.03961 (  524)
  hydrogen bonds       : angle       4.34257 ( 1518)
  link_BETA1-4         : bond        0.00152 (    2)
  link_BETA1-4         : angle       1.10607 (    6)
  link_NAG-ASN         : bond        0.00406 (    2)
  link_NAG-ASN         : angle       2.00816 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ASN cc_start: 0.9606 (m-40) cc_final: 0.9332 (m-40)
REVERT: A  498 ILE cc_start: 0.9267 (mt) cc_final: 0.9028 (mp)
REVERT: A  554 ASN cc_start: 0.9027 (t0) cc_final: 0.8581 (t0)
REVERT: A  559 MET cc_start: 0.8798 (mtm) cc_final: 0.8256 (mtt)
REVERT: A  617 MET cc_start: 0.8820 (mmm) cc_final: 0.8440 (mtm)
REVERT: A  681 GLU cc_start: 0.8947 (tt0) cc_final: 0.8432 (tm-30)
REVERT: A  705 ASP cc_start: 0.9357 (m-30) cc_final: 0.9080 (m-30)
REVERT: A  721 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8386 (mtp)
REVERT: A  759 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8369 (pm20)
REVERT: B  433 ASN cc_start: 0.9595 (m110) cc_final: 0.9294 (m110)
REVERT: B  554 ASN cc_start: 0.9051 (t0) cc_final: 0.8590 (t0)
REVERT: B  559 MET cc_start: 0.8812 (mtm) cc_final: 0.8291 (mtt)
REVERT: B  681 GLU cc_start: 0.8946 (tt0) cc_final: 0.8431 (tm-30)
REVERT: B  705 ASP cc_start: 0.9370 (m-30) cc_final: 0.9099 (m-30)
REVERT: B  721 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8564 (mmm)
  outliers start: 21
  outliers final: 8
  residues processed: 85
  average time/residue: 0.4050
  time to fit residues: 37.6759
Evaluate side-chains
  76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 521 GLN
A 819 HIS
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 819 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.056982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.048317 restraints weight = 30517.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 3.28
r_work: 0.2635 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8796  Z= 0.131
  Angle     :  0.608   9.669  11986  Z= 0.280
  Chirality :  0.039   0.160   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.768  59.967   1836
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.73 %
    Favored  : 84.15 %
  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:  1.98 (0.27), residues: 1022
  helix:  2.13 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.47 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 656 
 TYR   0.013   0.001   TYR A 824 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.016   0.001   TRP B 492 
 HIS   0.002   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8792)
  covalent geometry    : angle       0.60639 (11974)
  hydrogen bonds       : bond        0.03680 (  524)
  hydrogen bonds       : angle       4.27211 ( 1518)
  link_BETA1-4         : bond        0.00287 (    2)
  link_BETA1-4         : angle       1.02048 (    6)
  link_NAG-ASN         : bond        0.00238 (    2)
  link_NAG-ASN         : angle       1.88134 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ASN cc_start: 0.9602 (m-40) cc_final: 0.9309 (m-40)
REVERT: A  498 ILE cc_start: 0.9215 (mt) cc_final: 0.8991 (mp)
REVERT: A  554 ASN cc_start: 0.9004 (t0) cc_final: 0.8505 (t0)
REVERT: A  559 MET cc_start: 0.8842 (mtm) cc_final: 0.8317 (mtt)
REVERT: A  664 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8778 (mpp)
REVERT: A  681 GLU cc_start: 0.8913 (tt0) cc_final: 0.8243 (tt0)
REVERT: A  721 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8242 (mtp)
REVERT: A  759 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8331 (pm20)
REVERT: B  433 ASN cc_start: 0.9542 (m110) cc_final: 0.9184 (m110)
REVERT: B  522 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8965 (mm-30)
REVERT: B  554 ASN cc_start: 0.9019 (t0) cc_final: 0.8520 (t0)
REVERT: B  559 MET cc_start: 0.8815 (mtm) cc_final: 0.8289 (mtt)
REVERT: B  681 GLU cc_start: 0.8919 (tt0) cc_final: 0.8200 (tt0)
  outliers start: 19
  outliers final: 8
  residues processed: 80
  average time/residue: 0.3827
  time to fit residues: 33.7004
Evaluate side-chains
  79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 759 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 = 0.3031 r_free = 0.3031 target = 0.057190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.048615 restraints weight = 30048.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 3.24
r_work: 0.2645 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8796  Z= 0.128
  Angle     :  0.626  10.866  11986  Z= 0.286
  Chirality :  0.039   0.158   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.621  59.401   1836
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.17 %
    Favored  : 84.15 %
  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:  2.01 (0.27), residues: 1022
  helix:  2.17 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.48 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 490 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.012   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8792)
  covalent geometry    : angle       0.62401 (11974)
  hydrogen bonds       : bond        0.03616 (  524)
  hydrogen bonds       : angle       4.28436 ( 1518)
  link_BETA1-4         : bond        0.00257 (    2)
  link_BETA1-4         : angle       1.00377 (    6)
  link_NAG-ASN         : bond        0.00238 (    2)
  link_NAG-ASN         : angle       1.87748 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ASN cc_start: 0.9606 (m-40) cc_final: 0.9305 (m-40)
REVERT: A  554 ASN cc_start: 0.9027 (t0) cc_final: 0.8522 (t0)
REVERT: A  559 MET cc_start: 0.8814 (mtm) cc_final: 0.8330 (mtt)
REVERT: A  664 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8788 (mpp)
REVERT: A  681 GLU cc_start: 0.8908 (tt0) cc_final: 0.8224 (tt0)
REVERT: A  721 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8373 (mtp)
REVERT: A  759 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8380 (pm20)
REVERT: B  433 ASN cc_start: 0.9523 (m110) cc_final: 0.9144 (m110)
REVERT: B  522 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8966 (mm-30)
REVERT: B  554 ASN cc_start: 0.9035 (t0) cc_final: 0.8531 (t0)
REVERT: B  558 LEU cc_start: 0.9244 (mm) cc_final: 0.8999 (mm)
REVERT: B  559 MET cc_start: 0.8841 (mtm) cc_final: 0.8341 (mtt)
REVERT: B  681 GLU cc_start: 0.8897 (tt0) cc_final: 0.8149 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 79
  average time/residue: 0.3873
  time to fit residues: 33.5664
Evaluate side-chains
  77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 55 optimal weight:    0.4980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B 759 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 = 0.3009 r_free = 0.3009 target = 0.056244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.047489 restraints weight = 30450.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.28
r_work: 0.2618 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8796  Z= 0.177
  Angle     :  0.648  12.593  11986  Z= 0.302
  Chirality :  0.040   0.190   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.586  57.981   1836
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.96 %
    Favored  : 83.59 %
  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:  1.98 (0.27), residues: 1022
  helix:  2.13 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.47 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 656 
 TYR   0.013   0.001   TYR A 824 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.011   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8792)
  covalent geometry    : angle       0.64691 (11974)
  hydrogen bonds       : bond        0.03800 (  524)
  hydrogen bonds       : angle       4.38146 ( 1518)
  link_BETA1-4         : bond        0.00224 (    2)
  link_BETA1-4         : angle       1.01729 (    6)
  link_NAG-ASN         : bond        0.00353 (    2)
  link_NAG-ASN         : angle       1.92331 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ASN cc_start: 0.9608 (m-40) cc_final: 0.9303 (m-40)
REVERT: A  498 ILE cc_start: 0.9217 (mt) cc_final: 0.9009 (mp)
REVERT: A  554 ASN cc_start: 0.9041 (t0) cc_final: 0.8505 (t0)
REVERT: A  559 MET cc_start: 0.8823 (mtm) cc_final: 0.8336 (mtt)
REVERT: A  681 GLU cc_start: 0.8920 (tt0) cc_final: 0.8273 (tt0)
REVERT: A  721 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8574 (mtm)
REVERT: A  759 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8509 (pm20)
REVERT: B  433 ASN cc_start: 0.9527 (m110) cc_final: 0.9152 (m110)
REVERT: B  522 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8976 (mm-30)
REVERT: B  554 ASN cc_start: 0.9072 (t0) cc_final: 0.8556 (t0)
REVERT: B  559 MET cc_start: 0.8894 (mtm) cc_final: 0.8373 (mtt)
REVERT: B  681 GLU cc_start: 0.8905 (tt0) cc_final: 0.8346 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 76
  average time/residue: 0.3841
  time to fit residues: 32.1960
Evaluate side-chains
  76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0060
   chunk 49 optimal weight:    0.4980
   chunk 95 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** B 759 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 = 0.3038 r_free = 0.3038 target = 0.057383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.048749 restraints weight = 30237.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 3.27
r_work: 0.2658 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8796  Z= 0.123
  Angle     :  0.647  13.332  11986  Z= 0.298
  Chirality :  0.039   0.172   1434
  Planarity :  0.005   0.048   1408
  Dihedral  :  8.421  57.437   1836
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.29 %
    Favored  : 84.26 %
  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:  2.00 (0.27), residues: 1022
  helix:  2.17 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -0.47 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 656 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.015   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8792)
  covalent geometry    : angle       0.64534 (11974)
  hydrogen bonds       : bond        0.03631 (  524)
  hydrogen bonds       : angle       4.36810 ( 1518)
  link_BETA1-4         : bond        0.00244 (    2)
  link_BETA1-4         : angle       0.97588 (    6)
  link_NAG-ASN         : bond        0.00199 (    2)
  link_NAG-ASN         : angle       1.89408 (    6)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ASN cc_start: 0.9604 (m-40) cc_final: 0.9275 (m-40)
REVERT: A  554 ASN cc_start: 0.9040 (t0) cc_final: 0.8511 (t0)
REVERT: A  559 MET cc_start: 0.8789 (mtm) cc_final: 0.8313 (mtt)
REVERT: A  681 GLU cc_start: 0.8915 (tt0) cc_final: 0.8212 (tt0)
REVERT: A  721 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8306 (mtp)
REVERT: A  759 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: B  433 ASN cc_start: 0.9519 (m110) cc_final: 0.9138 (m110)
REVERT: B  522 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8904 (mm-30)
REVERT: B  554 ASN cc_start: 0.9042 (t0) cc_final: 0.8536 (t0)
REVERT: B  559 MET cc_start: 0.8884 (mtm) cc_final: 0.8370 (mtt)
REVERT: B  601 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8376 (tm)
REVERT: B  681 GLU cc_start: 0.8901 (tt0) cc_final: 0.8339 (tm-30)
REVERT: B  721 MET cc_start: 0.8746 (mmm) cc_final: 0.8017 (mpp)
  outliers start: 13
  outliers final: 7
  residues processed: 79
  average time/residue: 0.3889
  time to fit residues: 33.7940
Evaluate side-chains
  74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0070
   chunk 55 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 880 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.048870 restraints weight = 30478.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 3.29
r_work: 0.2666 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8796  Z= 0.132
  Angle     :  0.681  18.055  11986  Z= 0.308
  Chirality :  0.040   0.236   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.315  58.416   1836
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.73 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.98 (0.27), residues: 1022
  helix:  2.08 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -0.40 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 656 
 TYR   0.013   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.011   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8792)
  covalent geometry    : angle       0.67972 (11974)
  hydrogen bonds       : bond        0.03623 (  524)
  hydrogen bonds       : angle       4.37750 ( 1518)
  link_BETA1-4         : bond        0.00251 (    2)
  link_BETA1-4         : angle       0.97330 (    6)
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       1.88953 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2004.61 seconds
wall clock time: 35 minutes 6.44 seconds (2106.44 seconds total)