Starting phenix.real_space_refine
on Thu Jul  2 16:16:49 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty8_26169/07_2026/7ty8_26169.cif"
  }
  resolution = 3.18
  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=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    5800      2.51       5
     N    1314      2.21       5
     O    1433      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8591
  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 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 chiralities: 2
    Chain: "A"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 186
          Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 186
          Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
  Time building chain proxies: 2.08, per 1000 atoms: 0.24
  Number of scatterers: 8591
  At special positions: 0
  Unit cell: (125.892, 85.004, 83.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       2     15.00
     F       6      9.00
     O    1433      8.00
     N    1314      7.00
     C    5800      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: 0.98
  Conformation dependent library (CDL) restraints added in 315.6 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:
      56 helices and 4 sheets defined
      74.4% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 402 through 432
      removed outlier: 3.882A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
      removed outlier: 3.711A  pdb=" N   THR A 481 " --> pdb=" O   SER A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 4.143A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL A 502 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 516
      removed outlier: 3.527A  pdb=" N   VAL A 513 " --> pdb=" O   SER A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.901A  pdb=" N   ILE A 543 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.572A  pdb=" N   LEU A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.737A  pdb=" N   VAL A 604 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.526A  pdb=" N   MET A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A 621 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.595A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
      removed outlier: 3.741A  pdb=" N   ILE A 684 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 719
      removed outlier: 3.966A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 738
    Processing helix  chain 'A' and resid 760 through 773
      removed outlier: 3.584A  pdb=" N   ALA A 767 " --> pdb=" O   GLY A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.564A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 791 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 810
    Processing helix  chain 'A' and resid 811 through 813
      No H-bonds generated for 'chain 'A' and resid 811 through 813'
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.737A  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
      removed outlier: 3.604A  pdb=" N   LEU A 835 " --> pdb=" O   TRP A 831 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 852 " --> pdb=" O   TRP A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 864
    Processing helix  chain 'A' and resid 865 through 872
      removed outlier: 3.559A  pdb=" N   LEU A 869 " --> pdb=" O   LEU A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 878
    Processing helix  chain 'A' and resid 879 through 887
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 402 through 432
      removed outlier: 3.882A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
      removed outlier: 3.711A  pdb=" N   THR B 481 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 4.157A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 502 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE B 507 " --> pdb=" O   LEU B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.528A  pdb=" N   VAL B 513 " --> pdb=" O   SER B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.903A  pdb=" N   ILE B 543 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
      removed outlier: 3.565A  pdb=" N   LEU B 573 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 608
      removed outlier: 3.737A  pdb=" N   VAL B 604 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 3.525A  pdb=" N   MET B 617 " --> pdb=" O   SER B 613 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP B 621 " --> pdb=" O   MET B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 3.595A  pdb=" N   MET B 664 " --> pdb=" O   PRO B 660 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 665 " --> pdb=" O   ILE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 690
      removed outlier: 3.743A  pdb=" N   ILE B 684 " --> pdb=" O   LEU B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 3.964A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 727 through 738
    Processing helix  chain 'B' and resid 760 through 773
      removed outlier: 3.583A  pdb=" N   ALA B 767 " --> pdb=" O   GLY B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.564A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 791 " --> pdb=" O   VAL B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 810
    Processing helix  chain 'B' and resid 811 through 813
      No H-bonds generated for 'chain 'B' and resid 811 through 813'
    Processing helix  chain 'B' and resid 815 through 819
      removed outlier: 3.734A  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
      removed outlier: 3.605A  pdb=" N   LEU B 835 " --> pdb=" O   TRP B 831 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER B 852 " --> pdb=" O   TRP B 848 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 858 through 864
    Processing helix  chain 'B' and resid 865 through 872
      removed outlier: 3.556A  pdb=" N   LEU B 869 " --> pdb=" O   LEU B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 878
    Processing helix  chain 'B' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742
      removed outlier: 7.592A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 754 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742
      removed outlier: 7.591A  pdb=" N   VAL B 740 " --> pdb=" O   GLN B 754 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLN B 754 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1446 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: 1.34

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1392
        1.33 -     1.45: 2156
        1.45 -     1.58: 5174
        1.58 -     1.70: 4
        1.70 -     1.83: 66
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" N   ILE B 783 "
       pdb=" CA  ILE B 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 7.60e-03 1.73e+04 2.36e+01
  bond pdb=" N   ILE A 783 "
       pdb=" CA  ILE A 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 7.60e-03 1.73e+04 2.24e+01
  bond pdb=" N   VAL B 634 "
       pdb=" CA  VAL B 634 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 8.70e-03 1.32e+04 1.60e+01
  bond pdb=" N   VAL A 634 "
       pdb=" CA  VAL A 634 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 8.70e-03 1.32e+04 1.60e+01
  bond pdb=" N   LEU A 669 "
       pdb=" CA  LEU A 669 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 8.50e-03 1.38e+04 1.27e+01
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 7968
        1.64 -     3.28: 3171
        3.28 -     4.91: 728
        4.91 -     6.55: 108
        6.55 -     8.19: 5
  Bond angle restraints: 11980
  Sorted by residual:
  angle pdb=" C   PRO B 598 "
        pdb=" N   GLY B 599 "
        pdb=" CA  GLY B 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.80   -5.77 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  125.79   -5.76 1.12e+00 7.97e-01 2.65e+01
  angle pdb=" C   GLY B 380 "
        pdb=" N   GLY B 381 "
        pdb=" CA  GLY B 381 "
      ideal   model   delta    sigma   weight residual
     120.00  125.62   -5.62 1.10e+00 8.26e-01 2.61e+01
  angle pdb=" C   GLY A 380 "
        pdb=" N   GLY A 381 "
        pdb=" CA  GLY A 381 "
      ideal   model   delta    sigma   weight residual
     120.00  125.61   -5.61 1.10e+00 8.26e-01 2.60e+01
  angle pdb=" N   LEU A 873 "
        pdb=" CA  LEU A 873 "
        pdb=" C   LEU A 873 "
      ideal   model   delta    sigma   weight residual
     111.07  116.05   -4.98 1.07e+00 8.73e-01 2.17e+01
  ... (remaining 11975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 4582
       17.32 -    34.64: 355
       34.64 -    51.96: 97
       51.96 -    69.28: 31
       69.28 -    86.61: 11
  Dihedral angle restraints: 5076
    sinusoidal: 2106
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" CA  ARG A 388 "
           pdb=" C   ARG A 388 "
           pdb=" N   ARG A 389 "
           pdb=" CA  ARG A 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.60  -19.40     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ARG B 388 "
           pdb=" C   ARG B 388 "
           pdb=" N   ARG B 389 "
           pdb=" CA  ARG B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  TYR A 628 "
           pdb=" C   TYR A 628 "
           pdb=" N   THR A 629 "
           pdb=" CA  THR A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.42   16.58     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 5073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 488
       0.043 -    0.086: 398
       0.086 -    0.129: 366
       0.129 -    0.172: 163
       0.172 -    0.215: 19
  Chirality restraints: 1434
  Sorted by residual:
  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 1.16e+01
  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   -2.35   -0.05 2.00e-02 2.50e+03 7.08e+00
  chirality pdb=" CA  LEU B 484 "
            pdb=" N   LEU B 484 "
            pdb=" C   LEU B 484 "
            pdb=" CB  LEU B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.305 2.00e-02 2.50e+03   2.57e-01 8.25e+02
        pdb=" C7  NAG D   1 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.441 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.304 2.00e-02 2.50e+03   2.56e-01 8.21e+02
        pdb=" C7  NAG C   1 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.439 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "   -0.072 2.00e-02 2.50e+03   5.89e-02 4.33e+01
        pdb=" C7  NAG C   2 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "   -0.054 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "    0.093 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1401 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 2694
        2.91 -     3.40: 9413
        3.40 -     3.90: 15126
        3.90 -     4.40: 17228
        4.40 -     4.90: 28434
  Nonbonded interactions: 72895
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU B 874 "
            pdb=" CD2 PHE B 878 "
     model   vdw
     2.407 3.760
  nonbonded pdb=" CD1 LEU A 874 "
            pdb=" CD2 PHE A 878 "
     model   vdw
     2.430 3.760
  nonbonded pdb=" OH  TYR A 555 "
            pdb=" OH  TYR B 555 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   VAL B 729 "
            pdb=" OG1 THR B 733 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O   VAL A 729 "
            pdb=" OG1 THR A 733 "
     model   vdw
     2.486 3.040
  ... (remaining 72890 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: 0.02
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:             2.950
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.160
  Find NCS groups from input model:        0.140
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
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   0.049   8796  Z= 1.007
  Angle     :  1.783   8.189  11992  Z= 1.347
  Chirality :  0.085   0.215   1434
  Planarity :  0.010   0.257   1402
  Dihedral  : 14.761  86.606   3160
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.37 %
    Favored  : 91.85 %
  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: -3.38 (0.22), residues: 1022
  helix: -2.25 (0.16), residues: 676
  sheet:  None (None), residues: 0
  loop : -1.83 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 514 
 TYR   0.014   0.002   TYR B 628 
 PHE   0.016   0.002   PHE A 495 
 TRP   0.023   0.003   TRP B 662 
 HIS   0.004   0.001   HIS A 819 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01313 /  1.01 ( 8792)
  covalent geometry    : angle       1.78225 /  1.35 (11980)
  hydrogen bonds       : bond        0.24621 / 16.28 (  498)
  hydrogen bonds       : angle       8.76273 /  6.18 ( 1446)
  link_BETA1-4         : bond        0.00159 /  0.08 (    2)
  link_BETA1-4         : angle       0.40360 /  0.21 (    6)
  link_NAG-ASN         : bond        0.00136 /  0.07 (    2)
  link_NAG-ASN         : angle       3.69201 /  2.07 (    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
  208 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 201
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  641 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7207 (p)
REVERT: A  696 MET cc_start: 0.7845 (mmm) cc_final: 0.7569 (mmt)
REVERT: A  833 MET cc_start: 0.8496 (tmm) cc_final: 0.8162 (tmm)
REVERT: B  696 MET cc_start: 0.7842 (mmm) cc_final: 0.7558 (mmt)
REVERT: B  833 MET cc_start: 0.8457 (tmm) cc_final: 0.8101 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 208
  average time/residue: 0.0955
  time to fit residues: 27.5432
Evaluate side-chains
  115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  641 SER
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 550 GLN
A 683 GLN
B 550 GLN
B 683 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.082555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.074362 restraints weight = 28366.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.51
r_work: 0.3207 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8796  Z= 0.163
  Angle     :  0.651   6.790  11992  Z= 0.324
  Chirality :  0.042   0.164   1434
  Planarity :  0.005   0.041   1402
  Dihedral  : 10.610  88.566   1263
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.95 %
    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: -0.45 (0.25), residues: 1022
  helix:  0.23 (0.18), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.32 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 694 
 TYR   0.009   0.001   TYR A 486 
 PHE   0.022   0.002   PHE A 411 
 TRP   0.014   0.002   TRP A 662 
 HIS   0.004   0.001   HIS B 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.16 ( 8792)
  covalent geometry    : angle       0.65074 /  0.32 (11980)
  hydrogen bonds       : bond        0.05707 /  3.76 (  498)
  hydrogen bonds       : angle       4.70373 /  3.35 ( 1446)
  link_BETA1-4         : bond        0.00449 /  0.23 (    2)
  link_BETA1-4         : angle       0.94488 /  0.49 (    6)
  link_NAG-ASN         : bond        0.00478 /  0.24 (    2)
  link_NAG-ASN         : angle       1.15237 /  0.80 (    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
  139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  413 TYR cc_start: 0.9228 (t80) cc_final: 0.9017 (t80)
REVERT: A  812 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8619 (mp)
REVERT: B  399 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8050 (t0)
REVERT: B  413 TYR cc_start: 0.9241 (t80) cc_final: 0.9032 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 134
  average time/residue: 0.0589
  time to fit residues: 12.6725
Evaluate side-chains
  111 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 26 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 457 GLN
A 834 HIS
B 834 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.083582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.075506 restraints weight = 27635.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 3.44
r_work: 0.3240 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8796  Z= 0.126
  Angle     :  0.594   7.999  11992  Z= 0.289
  Chirality :  0.039   0.169   1434
  Planarity :  0.005   0.046   1402
  Dihedral  : 10.300  89.149   1258
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.50 %
    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:  0.49 (0.25), residues: 1022
  helix:  0.99 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.01 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 694 
 TYR   0.015   0.001   TYR B 486 
 PHE   0.017   0.001   PHE A 411 
 TRP   0.010   0.001   TRP A 662 
 HIS   0.002   0.001   HIS A 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8792)
  covalent geometry    : angle       0.59335 /  0.29 (11980)
  hydrogen bonds       : bond        0.04450 /  2.98 (  498)
  hydrogen bonds       : angle       4.41505 /  3.16 ( 1446)
  link_BETA1-4         : bond        0.00330 /  0.17 (    2)
  link_BETA1-4         : angle       0.69565 /  0.38 (    6)
  link_NAG-ASN         : bond        0.00150 /  0.08 (    2)
  link_NAG-ASN         : angle       1.40301 /  0.89 (    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
  148 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  399 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8234 (t70)
REVERT: A  486 TYR cc_start: 0.7792 (t80) cc_final: 0.7466 (t80)
REVERT: A  664 MET cc_start: 0.8409 (mtm) cc_final: 0.8099 (mtp)
REVERT: A  812 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: A  833 MET cc_start: 0.7108 (tmm) cc_final: 0.6837 (ppp)
REVERT: B  399 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8169 (t0)
REVERT: B  664 MET cc_start: 0.8366 (mtm) cc_final: 0.8088 (mtp)
REVERT: B  833 MET cc_start: 0.7043 (tmm) cc_final: 0.6833 (ppp)
  outliers start: 29
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0650
  time to fit residues: 14.0179
Evaluate side-chains
  117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  809 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 884 GLN
B 457 GLN
B 884 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.080634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.072702 restraints weight = 28721.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.45
r_work: 0.3202 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8796  Z= 0.173
  Angle     :  0.620   8.547  11992  Z= 0.298
  Chirality :  0.040   0.166   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  9.798  87.428   1258
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.51 %
    Favored  : 82.48 %
  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:  0.78 (0.26), residues: 1022
  helix:  1.14 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.73 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 490 
 TYR   0.022   0.001   TYR B 486 
 PHE   0.018   0.001   PHE A 836 
 TRP   0.010   0.001   TRP A 662 
 HIS   0.002   0.001   HIS A 547 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.17 ( 8792)
  covalent geometry    : angle       0.61955 /  0.30 (11980)
  hydrogen bonds       : bond        0.04365 /  2.92 (  498)
  hydrogen bonds       : angle       4.42824 /  3.16 ( 1446)
  link_BETA1-4         : bond        0.00330 /  0.16 (    2)
  link_BETA1-4         : angle       0.65001 /  0.41 (    6)
  link_NAG-ASN         : bond        0.00160 /  0.08 (    2)
  link_NAG-ASN         : angle       1.53571 /  1.04 (    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
  133 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  664 MET cc_start: 0.8396 (mtm) cc_final: 0.8024 (mtp)
REVERT: A  820 PRO cc_start: 0.8893 (Cg_exo) cc_final: 0.8623 (Cg_endo)
REVERT: B  486 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7550 (t80)
REVERT: B  664 MET cc_start: 0.8350 (mtm) cc_final: 0.7990 (mtp)
REVERT: B  833 MET cc_start: 0.7081 (tmm) cc_final: 0.6860 (ppp)
  outliers start: 27
  outliers final: 19
  residues processed: 123
  average time/residue: 0.0596
  time to fit residues: 11.7842
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.081188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.073436 restraints weight = 28298.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.37
r_work: 0.3202 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8796  Z= 0.136
  Angle     :  0.598   9.950  11992  Z= 0.286
  Chirality :  0.039   0.167   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  9.571  89.342   1258
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.62 %
    Favored  : 81.36 %
  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:  0.98 (0.26), residues: 1022
  helix:  1.26 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.58 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 694 
 TYR   0.021   0.001   TYR B 486 
 PHE   0.014   0.001   PHE B 836 
 TRP   0.009   0.001   TRP B 662 
 HIS   0.003   0.001   HIS A 834 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 8792)
  covalent geometry    : angle       0.59722 /  0.29 (11980)
  hydrogen bonds       : bond        0.04085 /  2.73 (  498)
  hydrogen bonds       : angle       4.33981 /  3.10 ( 1446)
  link_BETA1-4         : bond        0.00431 /  0.22 (    2)
  link_BETA1-4         : angle       0.72902 /  0.41 (    6)
  link_NAG-ASN         : bond        0.00063 /  0.03 (    2)
  link_NAG-ASN         : angle       1.42109 /  0.95 (    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
  136 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  664 MET cc_start: 0.8211 (mtm) cc_final: 0.7857 (mtp)
REVERT: A  812 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: A  820 PRO cc_start: 0.8775 (Cg_exo) cc_final: 0.8521 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7270 (ppp) cc_final: 0.7059 (tmm)
REVERT: B  664 MET cc_start: 0.8195 (mtm) cc_final: 0.7848 (mtp)
REVERT: B  833 MET cc_start: 0.7098 (tmm) cc_final: 0.6648 (tmm)
  outliers start: 27
  outliers final: 17
  residues processed: 129
  average time/residue: 0.0583
  time to fit residues: 12.1318
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0670
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.6518

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.081423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.073474 restraints weight = 28611.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.43
r_work: 0.3207 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8796  Z= 0.124
  Angle     :  0.600  10.597  11992  Z= 0.283
  Chirality :  0.040   0.168   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  9.414  89.413   1258
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.19 %
    Favored  : 80.58 %
  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:  1.20 (0.26), residues: 1022
  helix:  1.41 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.43 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 490 
 TYR   0.025   0.001   TYR B 486 
 PHE   0.013   0.001   PHE B 836 
 TRP   0.012   0.001   TRP A 662 
 HIS   0.001   0.000   HIS A 547 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.12 ( 8792)
  covalent geometry    : angle       0.59906 /  0.28 (11980)
  hydrogen bonds       : bond        0.03881 /  2.60 (  498)
  hydrogen bonds       : angle       4.26422 /  3.05 ( 1446)
  link_BETA1-4         : bond        0.00379 /  0.19 (    2)
  link_BETA1-4         : angle       0.76417 /  0.45 (    6)
  link_NAG-ASN         : bond        0.00035 /  0.02 (    2)
  link_NAG-ASN         : angle       1.35671 /  0.90 (    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
  133 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  664 MET cc_start: 0.8239 (mtm) cc_final: 0.7875 (mtp)
REVERT: A  812 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8633 (mp)
REVERT: A  820 PRO cc_start: 0.8801 (Cg_exo) cc_final: 0.8550 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7150 (ppp) cc_final: 0.6878 (tmm)
REVERT: B  617 MET cc_start: 0.8057 (mmm) cc_final: 0.7714 (mtp)
REVERT: B  664 MET cc_start: 0.8219 (mtm) cc_final: 0.7874 (mtp)
REVERT: B  820 PRO cc_start: 0.8754 (Cg_exo) cc_final: 0.8492 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7136 (tmm) cc_final: 0.6656 (tmm)
  outliers start: 20
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0586
  time to fit residues: 12.3997
Evaluate side-chains
  122 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  877 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0010
   chunk 42 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0270
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.3844

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.082638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.074762 restraints weight = 28564.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 3.46
r_work: 0.3230 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8796  Z= 0.113
  Angle     :  0.593  11.794  11992  Z= 0.280
  Chirality :  0.039   0.169   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  9.212  88.734   1258
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.75 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.26), residues: 1022
  helix:  1.53 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.35 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 694 
 TYR   0.024   0.001   TYR B 486 
 PHE   0.012   0.001   PHE A 524 
 TRP   0.015   0.001   TRP A 662 
 HIS   0.001   0.000   HIS A 547 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 8792)
  covalent geometry    : angle       0.59221 /  0.28 (11980)
  hydrogen bonds       : bond        0.03660 /  2.46 (  498)
  hydrogen bonds       : angle       4.20258 /  3.01 ( 1446)
  link_BETA1-4         : bond        0.00271 /  0.14 (    2)
  link_BETA1-4         : angle       0.70990 /  0.42 (    6)
  link_NAG-ASN         : bond        0.00041 /  0.02 (    2)
  link_NAG-ASN         : angle       1.28819 /  0.84 (    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
  132 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  587 MET cc_start: 0.8063 (mmp) cc_final: 0.7849 (mmp)
REVERT: A  664 MET cc_start: 0.8145 (mtm) cc_final: 0.7768 (mtp)
REVERT: A  812 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8637 (mp)
REVERT: A  820 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8564 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7226 (ppp) cc_final: 0.6934 (tmm)
REVERT: B  587 MET cc_start: 0.8146 (mmp) cc_final: 0.7932 (mmp)
REVERT: B  664 MET cc_start: 0.8076 (mtm) cc_final: 0.7720 (mtp)
REVERT: B  820 PRO cc_start: 0.8733 (Cg_exo) cc_final: 0.8475 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7163 (tmm) cc_final: 0.6669 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0606
  time to fit residues: 12.4372
Evaluate side-chains
  122 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0060
   overall best weight:    0.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 759 GLN
B 759 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.081785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.074047 restraints weight = 28474.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.35
r_work: 0.3219 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4115

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= 0.127
  Angle     :  0.609  12.749  11992  Z= 0.286
  Chirality :  0.040   0.190   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  9.047  88.126   1258
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.30 %
    Favored  : 79.02 %
  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:  1.48 (0.26), residues: 1022
  helix:  1.60 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.29 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 694 
 TYR   0.023   0.002   TYR B 486 
 PHE   0.012   0.001   PHE B 836 
 TRP   0.019   0.001   TRP B 662 
 HIS   0.001   0.001   HIS B 834 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 8792)
  covalent geometry    : angle       0.60823 /  0.29 (11980)
  hydrogen bonds       : bond        0.03811 /  2.56 (  498)
  hydrogen bonds       : angle       4.18460 /  3.00 ( 1446)
  link_BETA1-4         : bond        0.00298 /  0.15 (    2)
  link_BETA1-4         : angle       0.74692 /  0.46 (    6)
  link_NAG-ASN         : bond        0.00083 /  0.04 (    2)
  link_NAG-ASN         : angle       1.35350 /  0.89 (    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
  126 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8831 (t)
REVERT: A  587 MET cc_start: 0.8120 (mmp) cc_final: 0.7913 (mmp)
REVERT: A  664 MET cc_start: 0.8090 (mtm) cc_final: 0.7744 (mtp)
REVERT: A  812 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8752 (mp)
REVERT: A  820 PRO cc_start: 0.8748 (Cg_exo) cc_final: 0.8521 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7287 (ppp) cc_final: 0.6962 (tmm)
REVERT: B  513 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8834 (t)
REVERT: B  587 MET cc_start: 0.8330 (mmp) cc_final: 0.8105 (mmp)
REVERT: B  664 MET cc_start: 0.8087 (mtm) cc_final: 0.7742 (mtp)
REVERT: B  820 PRO cc_start: 0.8764 (Cg_exo) cc_final: 0.8512 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7168 (tmm) cc_final: 0.6645 (tmm)
  outliers start: 24
  outliers final: 18
  residues processed: 119
  average time/residue: 0.0637
  time to fit residues: 12.2887
Evaluate side-chains
  122 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6538

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.081935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074081 restraints weight = 28551.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.46
r_work: 0.3219 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8796  Z= 0.123
  Angle     :  0.609  13.022  11992  Z= 0.285
  Chirality :  0.039   0.179   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.958  87.341   1258
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.19 %
    Favored  : 79.24 %
  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:  1.61 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.22 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 646 
 TYR   0.028   0.002   TYR B 486 
 PHE   0.016   0.001   PHE B 836 
 TRP   0.025   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.12 ( 8792)
  covalent geometry    : angle       0.60829 /  0.28 (11980)
  hydrogen bonds       : bond        0.03687 /  2.48 (  498)
  hydrogen bonds       : angle       4.17410 /  3.00 ( 1446)
  link_BETA1-4         : bond        0.00375 /  0.18 (    2)
  link_BETA1-4         : angle       0.81368 /  0.51 (    6)
  link_NAG-ASN         : bond        0.00064 /  0.03 (    2)
  link_NAG-ASN         : angle       1.31343 /  0.86 (    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
  125 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8814 (t)
REVERT: A  587 MET cc_start: 0.8186 (mmp) cc_final: 0.7967 (mmp)
REVERT: A  664 MET cc_start: 0.8112 (mtm) cc_final: 0.7778 (mtp)
REVERT: A  812 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8655 (mp)
REVERT: A  820 PRO cc_start: 0.8718 (Cg_exo) cc_final: 0.8495 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7322 (ppp) cc_final: 0.6987 (tmm)
REVERT: B  513 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8809 (t)
REVERT: B  587 MET cc_start: 0.8415 (mmp) cc_final: 0.8183 (mmp)
REVERT: B  664 MET cc_start: 0.8093 (mtm) cc_final: 0.7765 (mtp)
REVERT: B  820 PRO cc_start: 0.8644 (Cg_exo) cc_final: 0.8403 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7129 (tmm) cc_final: 0.6609 (tmm)
  outliers start: 23
  outliers final: 20
  residues processed: 121
  average time/residue: 0.0623
  time to fit residues: 12.3061
Evaluate side-chains
  120 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 69 optimal weight:    0.3980
   chunk 77 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0170
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0570
   overall best weight:    0.2274

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.083132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.075290 restraints weight = 28801.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.41
r_work: 0.3250 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.4340

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= 0.113
  Angle     :  0.606  13.404  11992  Z= 0.284
  Chirality :  0.039   0.181   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.909  86.776   1258
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.75 %
    Favored  : 78.79 %
  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:  1.60 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.19 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 694 
 TYR   0.028   0.001   TYR B 486 
 PHE   0.018   0.001   PHE B 836 
 TRP   0.024   0.001   TRP A 662 
 HIS   0.001   0.001   HIS B 834 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 8792)
  covalent geometry    : angle       0.60581 /  0.28 (11980)
  hydrogen bonds       : bond        0.03570 /  2.39 (  498)
  hydrogen bonds       : angle       4.18833 /  3.02 ( 1446)
  link_BETA1-4         : bond        0.00349 /  0.18 (    2)
  link_BETA1-4         : angle       0.76744 /  0.46 (    6)
  link_NAG-ASN         : bond        0.00051 /  0.03 (    2)
  link_NAG-ASN         : angle       1.22584 /  0.81 (    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
  131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8820 (t)
REVERT: A  587 MET cc_start: 0.8285 (mmp) cc_final: 0.7966 (mmp)
REVERT: A  664 MET cc_start: 0.8001 (mtm) cc_final: 0.7620 (mtp)
REVERT: A  812 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: A  820 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8573 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7330 (ppp) cc_final: 0.6993 (tmm)
REVERT: B  513 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8809 (t)
REVERT: B  587 MET cc_start: 0.8432 (mmp) cc_final: 0.8211 (mmp)
REVERT: B  664 MET cc_start: 0.7907 (mtm) cc_final: 0.7529 (mtp)
REVERT: B  820 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8418 (Cg_endo)
  outliers start: 22
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0623
  time to fit residues: 13.0266
Evaluate side-chains
  123 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain A residue  841 ILE
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0040
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6592

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.082627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.074702 restraints weight = 28576.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 3.48
r_work: 0.3236 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8796  Z= 0.127
  Angle     :  0.631  13.521  11992  Z= 0.293
  Chirality :  0.039   0.175   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.913  86.582   1258
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.75 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.26), residues: 1022
  helix:  1.66 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.15 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 694 
 TYR   0.028   0.002   TYR B 486 
 PHE   0.016   0.001   PHE B 836 
 TRP   0.026   0.001   TRP A 662 
 HIS   0.003   0.001   HIS B 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 8792)
  covalent geometry    : angle       0.63010 /  0.29 (11980)
  hydrogen bonds       : bond        0.03701 /  2.48 (  498)
  hydrogen bonds       : angle       4.17467 /  3.00 ( 1446)
  link_BETA1-4         : bond        0.00282 /  0.14 (    2)
  link_BETA1-4         : angle       0.76802 /  0.47 (    6)
  link_NAG-ASN         : bond        0.00070 /  0.03 (    2)
  link_NAG-ASN         : angle       1.29795 /  0.84 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2006.88 seconds
wall clock time: 35 minutes 19.07 seconds (2119.07 seconds total)