Starting phenix.real_space_refine
on Sun Jun  8 04:43:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty8_26169/06_2025/7ty8_26169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty8_26169/06_2025/7ty8_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_26169/06_2025/7ty8_26169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty8_26169/06_2025/7ty8_26169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty8_26169/06_2025/7ty8_26169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty8_26169/06_2025/7ty8_26169.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 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: 6.49, per 1000 atoms: 0.76
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.92
  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: 2.41

  Time building geometry restraints manager: 2.86 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: 5094
       17.32 -    34.64: 380
       34.64 -    51.96: 106
       51.96 -    69.28: 33
       69.28 -    86.61: 13
  Dihedral angle restraints: 5626
    sinusoidal: 2656
      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 5623 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: 0.00
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:             2.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.560
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
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  : 14.152  86.606   3710
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (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
 TRP   0.023   0.003   TRP B 662 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.016   0.002   PHE A 495 
 TYR   0.014   0.002   TYR B 628 
 ARG   0.004   0.001   ARG B 514 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    2)
  link_NAG-ASN         : angle       3.69201 (    6)
  link_BETA1-4         : bond        0.00159 (    2)
  link_BETA1-4         : angle       0.40360 (    6)
  hydrogen bonds       : bond        0.24621 (  498)
  hydrogen bonds       : angle       8.76273 ( 1446)
  covalent geometry    : bond        0.01313 ( 8792)
  covalent geometry    : angle       1.78225 (11980)

*********************** 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  : 0.939 
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: 0.7568 (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: 0.7557 (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: 0.2119
  time to fit residues: 60.0143
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  : 0.925 
-------------------------------------------------------------------------------
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 86 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3524 r_free = 0.3524 target = 0.082699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074812 restraints weight = 27660.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.35
r_work: 0.3219 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2543

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= 0.158
  Angle     :  0.657   7.021  11992  Z= 0.325
  Chirality :  0.042   0.160   1434
  Planarity :  0.005   0.042   1402
  Dihedral  : 10.323  88.605   1813
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.61 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1022
  helix:  0.37 (0.18), residues: 700
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 492 
 HIS   0.004   0.001   HIS B 651 
 PHE   0.024   0.002   PHE A 411 
 TYR   0.010   0.001   TYR A 486 
 ARG   0.006   0.001   ARG A 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    2)
  link_NAG-ASN         : angle       1.10242 (    6)
  link_BETA1-4         : bond        0.00083 (    2)
  link_BETA1-4         : angle       0.95046 (    6)
  hydrogen bonds       : bond        0.05278 (  498)
  hydrogen bonds       : angle       4.64634 ( 1446)
  covalent geometry    : bond        0.00366 ( 8792)
  covalent geometry    : angle       0.65620 (11980)

*********************** 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
  149 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A  399 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8035 (t0)
REVERT: A  413 TYR cc_start: 0.9216 (t80) cc_final: 0.8992 (t80)
REVERT: A  812 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8641 (mp)
REVERT: B  399 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8038 (t0)
REVERT: B  413 TYR cc_start: 0.9252 (t80) cc_final: 0.9051 (t80)
REVERT: B  681 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8356 (mm-30)
  outliers start: 19
  outliers final: 6
  residues processed: 143
  average time/residue: 0.1515
  time to fit residues: 33.4581
Evaluate side-chains
  112 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  614 ILE
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  418 SER
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  681 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0970
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 834 HIS
B 834 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.083298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.075129 restraints weight = 28105.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.47
r_work: 0.3243 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8796  Z= 0.131
  Angle     :  0.602   7.668  11992  Z= 0.293
  Chirality :  0.039   0.165   1434
  Planarity :  0.005   0.046   1402
  Dihedral  : 10.011  89.677   1808
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.73 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1022
  helix:  0.94 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -1.15 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 662 
 HIS   0.002   0.001   HIS A 734 
 PHE   0.015   0.001   PHE A 836 
 TYR   0.014   0.001   TYR B 486 
 ARG   0.005   0.000   ARG A 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    2)
  link_NAG-ASN         : angle       1.43209 (    6)
  link_BETA1-4         : bond        0.00474 (    2)
  link_BETA1-4         : angle       0.71370 (    6)
  hydrogen bonds       : bond        0.04589 (  498)
  hydrogen bonds       : angle       4.44611 ( 1446)
  covalent geometry    : bond        0.00307 ( 8792)
  covalent geometry    : angle       0.60096 (11980)

*********************** 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
  138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  413 TYR cc_start: 0.9176 (t80) cc_final: 0.8936 (t80)
REVERT: A  664 MET cc_start: 0.8549 (mtm) cc_final: 0.8252 (mtp)
REVERT: A  812 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8578 (mp)
REVERT: B  399 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8110 (t0)
REVERT: B  413 TYR cc_start: 0.9178 (t80) cc_final: 0.8938 (t80)
REVERT: B  664 MET cc_start: 0.8496 (mtm) cc_final: 0.8199 (mtp)
REVERT: B  681 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8272 (mm-30)
  outliers start: 26
  outliers final: 13
  residues processed: 130
  average time/residue: 0.1536
  time to fit residues: 30.7598
Evaluate side-chains
  116 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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  449 ILE
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 B residue  397 ILE
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  449 ILE
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  681 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 457 GLN
A 884 GLN
B 457 GLN
B 884 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.082216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.074069 restraints weight = 28240.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 3.48
r_work: 0.3227 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8796  Z= 0.136
  Angle     :  0.601   8.435  11992  Z= 0.289
  Chirality :  0.039   0.164   1434
  Planarity :  0.005   0.049   1402
  Dihedral  :  9.582  81.164   1808
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.73 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1022
  helix:  1.13 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.76 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.014   0.001   PHE A 524 
 TYR   0.023   0.001   TYR B 486 
 ARG   0.003   0.001   ARG A 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    2)
  link_NAG-ASN         : angle       1.41175 (    6)
  link_BETA1-4         : bond        0.00251 (    2)
  link_BETA1-4         : angle       0.63716 (    6)
  hydrogen bonds       : bond        0.04267 (  498)
  hydrogen bonds       : angle       4.41636 ( 1446)
  covalent geometry    : bond        0.00322 ( 8792)
  covalent geometry    : angle       0.60001 (11980)

*********************** 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: 28
    poor density    : 105
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8263 (t70)
REVERT: A  664 MET cc_start: 0.8387 (mtm) cc_final: 0.8010 (mtp)
REVERT: B  399 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8298 (t70)
REVERT: B  664 MET cc_start: 0.8318 (mtm) cc_final: 0.7961 (mtp)
  outliers start: 28
  outliers final: 17
  residues processed: 126
  average time/residue: 0.1501
  time to fit residues: 29.4688
Evaluate side-chains
  120 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
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  620 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
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  759 GLN
Chi-restraints excluded: chain B residue  874 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0060
   chunk 87 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.082301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.074421 restraints weight = 28214.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.42
r_work: 0.3227 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8796  Z= 0.124
  Angle     :  0.598   9.407  11992  Z= 0.284
  Chirality :  0.039   0.164   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  9.373  81.776   1808
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.63 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1022
  helix:  1.33 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 662 
 HIS   0.001   0.000   HIS A 651 
 PHE   0.013   0.001   PHE A 411 
 TYR   0.022   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00029 (    2)
  link_NAG-ASN         : angle       1.31873 (    6)
  link_BETA1-4         : bond        0.00311 (    2)
  link_BETA1-4         : angle       0.68568 (    6)
  hydrogen bonds       : bond        0.03985 (  498)
  hydrogen bonds       : angle       4.33492 ( 1446)
  covalent geometry    : bond        0.00292 ( 8792)
  covalent geometry    : angle       0.59762 (11980)

*********************** 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
  134 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  399 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8330 (t70)
REVERT: A  664 MET cc_start: 0.8248 (mtm) cc_final: 0.7885 (mtp)
REVERT: A  812 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8606 (mp)
REVERT: A  820 PRO cc_start: 0.8745 (Cg_exo) cc_final: 0.8491 (Cg_endo)
REVERT: B  399 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8360 (t70)
REVERT: B  664 MET cc_start: 0.8213 (mtm) cc_final: 0.7860 (mtp)
  outliers start: 23
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1578
  time to fit residues: 30.2676
Evaluate side-chains
  119 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  405 VAL
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 A residue  812 LEU
Chi-restraints excluded: chain B residue  399 ASP
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.081669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.073702 restraints weight = 28288.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.40
r_work: 0.3224 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8796  Z= 0.131
  Angle     :  0.598  10.321  11992  Z= 0.283
  Chirality :  0.039   0.163   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  9.218  82.713   1808
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.18 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.26), residues: 1022
  helix:  1.44 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.45 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 662 
 HIS   0.004   0.001   HIS B 834 
 PHE   0.013   0.001   PHE A 836 
 TYR   0.020   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    2)
  link_NAG-ASN         : angle       1.33882 (    6)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       0.69825 (    6)
  hydrogen bonds       : bond        0.03934 (  498)
  hydrogen bonds       : angle       4.27646 ( 1446)
  covalent geometry    : bond        0.00310 ( 8792)
  covalent geometry    : angle       0.59734 (11980)

*********************** 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
  142 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  399 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8384 (t70)
REVERT: A  664 MET cc_start: 0.8235 (mtm) cc_final: 0.7857 (mtp)
REVERT: A  812 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: A  820 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8554 (Cg_endo)
REVERT: B  587 MET cc_start: 0.8203 (mmp) cc_final: 0.7994 (mmp)
REVERT: B  664 MET cc_start: 0.8241 (mtm) cc_final: 0.7882 (mtp)
REVERT: B  820 PRO cc_start: 0.8787 (Cg_exo) cc_final: 0.8525 (Cg_endo)
  outliers start: 28
  outliers final: 20
  residues processed: 131
  average time/residue: 0.1561
  time to fit residues: 33.1864
Evaluate side-chains
  128 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  405 VAL
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  620 VAL
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  418 SER
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  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.082043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.074205 restraints weight = 28388.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 3.47
r_work: 0.3228 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3888

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= 0.128
  Angle     :  0.605  11.150  11992  Z= 0.284
  Chirality :  0.039   0.164   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  8.995  82.957   1808
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.86 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1022
  helix:  1.49 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.39 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 662 
 HIS   0.002   0.001   HIS A 834 
 PHE   0.011   0.001   PHE B 836 
 TYR   0.024   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00029 (    2)
  link_NAG-ASN         : angle       1.30797 (    6)
  link_BETA1-4         : bond        0.00298 (    2)
  link_BETA1-4         : angle       0.73540 (    6)
  hydrogen bonds       : bond        0.03822 (  498)
  hydrogen bonds       : angle       4.22757 ( 1446)
  covalent geometry    : bond        0.00304 ( 8792)
  covalent geometry    : angle       0.60393 (11980)

*********************** 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
  130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  399 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8420 (t70)
REVERT: A  587 MET cc_start: 0.8215 (mmp) cc_final: 0.7981 (mmp)
REVERT: A  617 MET cc_start: 0.7522 (mmm) cc_final: 0.7295 (mtp)
REVERT: A  664 MET cc_start: 0.8185 (mtm) cc_final: 0.7797 (mtp)
REVERT: A  812 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8581 (mp)
REVERT: A  820 PRO cc_start: 0.8818 (Cg_exo) cc_final: 0.8572 (Cg_endo)
REVERT: B  513 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8799 (t)
REVERT: B  578 MET cc_start: 0.8853 (ttt) cc_final: 0.8517 (ttt)
REVERT: B  587 MET cc_start: 0.8118 (mmp) cc_final: 0.7897 (mmp)
REVERT: B  664 MET cc_start: 0.8180 (mtm) cc_final: 0.7808 (mtp)
REVERT: B  820 PRO cc_start: 0.8739 (Cg_exo) cc_final: 0.8476 (Cg_endo)
  outliers start: 23
  outliers final: 17
  residues processed: 124
  average time/residue: 0.1816
  time to fit residues: 35.8975
Evaluate side-chains
  124 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
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  759 GLN
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 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  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0010
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.082283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.074306 restraints weight = 28751.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 3.50
r_work: 0.3225 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8796  Z= 0.118
  Angle     :  0.610  12.886  11992  Z= 0.285
  Chirality :  0.039   0.164   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  8.721  82.355   1808
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.52 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1022
  helix:  1.51 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.31 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 662 
 HIS   0.002   0.001   HIS A 834 
 PHE   0.011   0.001   PHE A 524 
 TYR   0.024   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    2)
  link_NAG-ASN         : angle       1.26986 (    6)
  link_BETA1-4         : bond        0.00283 (    2)
  link_BETA1-4         : angle       0.73938 (    6)
  hydrogen bonds       : bond        0.03705 (  498)
  hydrogen bonds       : angle       4.18313 ( 1446)
  covalent geometry    : bond        0.00276 ( 8792)
  covalent geometry    : angle       0.60968 (11980)

*********************** 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
  133 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  399 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8440 (t70)
REVERT: A  513 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8810 (t)
REVERT: A  587 MET cc_start: 0.8115 (mmp) cc_final: 0.7753 (mmp)
REVERT: A  664 MET cc_start: 0.8090 (mtm) cc_final: 0.7706 (mtp)
REVERT: A  812 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8650 (mp)
REVERT: A  820 PRO cc_start: 0.8827 (Cg_exo) cc_final: 0.8590 (Cg_endo)
REVERT: B  513 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8798 (t)
REVERT: B  578 MET cc_start: 0.8866 (ttt) cc_final: 0.8431 (ttt)
REVERT: B  587 MET cc_start: 0.8197 (mmp) cc_final: 0.7965 (mmp)
REVERT: B  664 MET cc_start: 0.8131 (mtm) cc_final: 0.7775 (mtp)
REVERT: B  820 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8487 (Cg_endo)
  outliers start: 25
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1553
  time to fit residues: 30.4211
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  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
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  558 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  759 GLN
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 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  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.081606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.073858 restraints weight = 28557.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 3.35
r_work: 0.3217 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4135

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= 0.131
  Angle     :  0.620  12.635  11992  Z= 0.290
  Chirality :  0.040   0.176   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.591  81.633   1808
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.08 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1022
  helix:  1.50 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.25 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 662 
 HIS   0.001   0.001   HIS B 547 
 PHE   0.013   0.001   PHE B 836 
 TYR   0.024   0.001   TYR B 486 
 ARG   0.002   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    2)
  link_NAG-ASN         : angle       1.31447 (    6)
  link_BETA1-4         : bond        0.00237 (    2)
  link_BETA1-4         : angle       0.75929 (    6)
  hydrogen bonds       : bond        0.03789 (  498)
  hydrogen bonds       : angle       4.19931 ( 1446)
  covalent geometry    : bond        0.00313 ( 8792)
  covalent geometry    : angle       0.61970 (11980)

*********************** 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
  123 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8837 (t)
REVERT: A  587 MET cc_start: 0.8155 (mmp) cc_final: 0.7825 (mmp)
REVERT: A  664 MET cc_start: 0.8066 (mtm) cc_final: 0.7713 (mtp)
REVERT: A  812 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8703 (mp)
REVERT: A  820 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8509 (Cg_endo)
REVERT: B  513 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8820 (t)
REVERT: B  578 MET cc_start: 0.8875 (ttt) cc_final: 0.8499 (ttt)
REVERT: B  587 MET cc_start: 0.8284 (mmp) cc_final: 0.8034 (mmp)
REVERT: B  617 MET cc_start: 0.6492 (mtp) cc_final: 0.6273 (mtm)
REVERT: B  664 MET cc_start: 0.8014 (mtm) cc_final: 0.7650 (mtp)
REVERT: B  820 PRO cc_start: 0.8777 (Cg_exo) cc_final: 0.8532 (Cg_endo)
  outliers start: 22
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1674
  time to fit residues: 32.3393
Evaluate side-chains
  117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
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 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  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.081913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.073961 restraints weight = 28317.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.41
r_work: 0.3225 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4241

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= 0.126
  Angle     :  0.625  13.357  11992  Z= 0.291
  Chirality :  0.040   0.181   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  8.500  81.152   1808
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.53 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1022
  helix:  1.51 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.20 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE B 524 
 TYR   0.024   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00046 (    2)
  link_NAG-ASN         : angle       1.29811 (    6)
  link_BETA1-4         : bond        0.00262 (    2)
  link_BETA1-4         : angle       0.76109 (    6)
  hydrogen bonds       : bond        0.03760 (  498)
  hydrogen bonds       : angle       4.18668 ( 1446)
  covalent geometry    : bond        0.00298 ( 8792)
  covalent geometry    : angle       0.62394 (11980)

********************** 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
  120 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 1.683 
Fit side-chains
REVERT: A  399 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8283 (t70)
REVERT: A  513 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8847 (t)
REVERT: A  587 MET cc_start: 0.8217 (mmp) cc_final: 0.7908 (mmp)
REVERT: A  664 MET cc_start: 0.8027 (mtm) cc_final: 0.7645 (mtp)
REVERT: A  812 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: A  820 PRO cc_start: 0.8720 (Cg_exo) cc_final: 0.8493 (Cg_endo)
REVERT: B  513 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (t)
REVERT: B  578 MET cc_start: 0.8855 (ttt) cc_final: 0.8454 (ttt)
REVERT: B  587 MET cc_start: 0.8285 (mmp) cc_final: 0.8029 (mmp)
REVERT: B  664 MET cc_start: 0.7966 (mtm) cc_final: 0.7592 (mtp)
REVERT: B  820 PRO cc_start: 0.8671 (Cg_exo) cc_final: 0.8436 (Cg_endo)
  outliers start: 21
  outliers final: 16
  residues processed: 118
  average time/residue: 0.1704
  time to fit residues: 32.9160
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  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
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  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 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  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   chunk 96 optimal weight:    0.3980
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0470
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.3876

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.083161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.075164 restraints weight = 28398.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.46
r_work: 0.3249 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4366

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= 0.115
  Angle     :  0.625  13.504  11992  Z= 0.290
  Chirality :  0.040   0.165   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.352  79.908   1808
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.26), residues: 1022
  helix:  1.56 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.20 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE B 524 
 TYR   0.028   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00042 (    2)
  link_NAG-ASN         : angle       1.21686 (    6)
  link_BETA1-4         : bond        0.00297 (    2)
  link_BETA1-4         : angle       0.76249 (    6)
  hydrogen bonds       : bond        0.03650 (  498)
  hydrogen bonds       : angle       4.20470 ( 1446)
  covalent geometry    : bond        0.00264 ( 8792)
  covalent geometry    : angle       0.62400 (11980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5051.22 seconds
wall clock time: 90 minutes 45.16 seconds (5445.16 seconds total)