Starting phenix.real_space_refine
on Wed Feb  4 15:15:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gtu_51567/02_2026/9gtu_51567_trim.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    3495      2.51       5
     N     964      2.21       5
     O    1120      1.98       5
     H    5388      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11001
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "C"
      Number of atoms: 7088
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 454, 7046
          Classifications: {'peptide': 454}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 431}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 454, 7046
          Classifications: {'peptide': 454}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 431}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 7064
    Chain: "B"
      Number of atoms: 3455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 3455
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 216}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 311
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 3, 'TRANS': 21}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 29
          Classifications: {'water': 29}
          Link IDs: {None: 28}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
  Time building chain proxies: 3.14, per 1000 atoms: 0.29
  Number of scatterers: 11001
  At special positions: 0
  Unit cell: (72.912, 85.932, 96.348, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     O    1120      8.00
     N     964      7.00
     C    3495      6.00
     H    5388      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C2377 " - pdb=" SG  CYS C2591 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C2387 " - pdb=" SG  CYS B 602 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C2396 " - pdb=" SG  CYS C2587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C2439 " - pdb=" SG  CYS B 604 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C2584 " - pdb=" SG  CYS C2597 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 818 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 605 " - pdb=" SG  CYS A 606 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 827 " - pdb=" SG  CYS B1019 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG E   1 " - " FUC E   3 "
    NAG-ASN
      " NAG B1101 " - " ASN B 954 "
      " NAG C2901 " - " ASN C2677 "
      " NAG D   1 " - " ASN C2558 "
      " NAG E   1 " - " ASN B 897 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 483.0 milliseconds
  

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1334

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      42.4% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'C' and resid 2375 through 2384
    Processing helix  chain 'C' and resid 2414 through 2432
    Processing helix  chain 'C' and resid 2459 through 2463
      removed outlier: 3.592A  pdb=" N   SER C2463 " --> pdb=" O   PHE C2460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2465 through 2476
    Processing helix  chain 'C' and resid 2486 through 2497
    Processing helix  chain 'C' and resid 2523 through 2537
      removed outlier: 3.733A  pdb=" N   ARG C2527 " --> pdb=" O   SER C2523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2548 through 2555
      removed outlier: 3.538A  pdb=" N   ILE C2552 " --> pdb=" O   ASP C2548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2573 through 2584
      removed outlier: 4.063A  pdb=" N   PHE C2577 " --> pdb=" O   ASP C2573 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   CYS C2584 " --> pdb=" O   ASN C2580 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2631 through 2648
    Processing helix  chain 'C' and resid 2688 through 2692
      removed outlier: 4.556A  pdb=" N   TYR C2692 " --> pdb=" O   LEU C2689 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2694 through 2705
    Processing helix  chain 'C' and resid 2714 through 2726
    Processing helix  chain 'C' and resid 2748 through 2765
      removed outlier: 3.810A  pdb=" N   GLU C2753 " --> pdb=" O   GLU C2749 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   GLU C2754 " --> pdb=" O   GLN C2750 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2782 through 2787
      removed outlier: 3.647A  pdb=" N   THR C2785 " --> pdb=" O   GLU C2782 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA C2787 " --> pdb=" O   TYR C2784 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2790 through 2794
    Processing helix  chain 'C' and resid 2800 through 2805
    Processing helix  chain 'C' and resid 2806 through 2820
      removed outlier: 3.936A  pdb=" N   PHE C2812 " --> pdb=" O   PRO C2808 " (cutoff:3.500A)
      Proline residue:  C2817  - end of helix
    Processing helix  chain 'B' and resid 590 through 602
    Processing helix  chain 'B' and resid 846 through 863
    Processing helix  chain 'B' and resid 897 through 908
    Processing helix  chain 'B' and resid 916 through 928
    Processing helix  chain 'B' and resid 956 through 967
    Processing helix  chain 'B' and resid 981 through 989
    Processing helix  chain 'B' and resid 1001 through 1006
      removed outlier: 4.206A  pdb=" N   LEU B1005 " --> pdb=" O   TYR B1002 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1007 through 1019
    Processing helix  chain 'A' and resid 593 through 604
    Processing sheet with id=AA1, first strand: chain 'C' and resid 2454 through 2456
      removed outlier: 6.668A  pdb=" N   THR C2401 " --> pdb=" O   ARG C2444 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   ALA C2446 " --> pdb=" O   THR C2401 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU C2403 " --> pdb=" O   ALA C2446 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL C2448 " --> pdb=" O   LEU C2403 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   PHE C2405 " --> pdb=" O   VAL C2448 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TYR C2450 " --> pdb=" O   PHE C2405 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   LEU C2407 " --> pdb=" O   TYR C2450 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   GLU C2402 " --> pdb=" O   VAL C2511 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL C2513 " --> pdb=" O   GLU C2402 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA C2404 " --> pdb=" O   VAL C2513 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   PHE C2515 " --> pdb=" O   ALA C2404 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ALA C2406 " --> pdb=" O   PHE C2515 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   LYS C2510 " --> pdb=" O   THR C2539 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   LEU C2541 " --> pdb=" O   LYS C2510 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ALA C2512 " --> pdb=" O   LEU C2541 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU C2543 " --> pdb=" O   ALA C2512 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   PHE C2514 " --> pdb=" O   LEU C2543 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   HIS C2564 " --> pdb=" O   ILE C2538 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   LEU C2566 " --> pdb=" O   PRO C2540 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   PHE C2542 " --> pdb=" O   LEU C2566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 2684 through 2687
      removed outlier: 6.793A  pdb=" N   VAL C2666 " --> pdb=" O   GLU C2686 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET C2620 " --> pdb=" O   ALA C2665 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   VAL C2667 " --> pdb=" O   MET C2620 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   PHE C2622 " --> pdb=" O   VAL C2667 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ASP C2619 " --> pdb=" O   ILE C2738 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   VAL C2740 " --> pdb=" O   ASP C2619 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ALA C2621 " --> pdb=" O   VAL C2740 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LYS C2796 " --> pdb=" O   PHE C2769 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL C2771 " --> pdb=" O   LYS C2796 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   VAL C2798 " --> pdb=" O   VAL C2771 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLY C2773 " --> pdb=" O   VAL C2798 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 889 through 895
      removed outlier: 6.726A  pdb=" N   ALA B 891 " --> pdb=" O   GLN B 881 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   GLN B 881 " --> pdb=" O   ALA B 891 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   LEU B 879 " --> pdb=" O   PRO B 893 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASP B 833 " --> pdb=" O   SER B 943 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   VAL B 945 " --> pdb=" O   ASP B 833 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL B 835 " --> pdb=" O   VAL B 945 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU B 947 " --> pdb=" O   VAL B 835 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B 837 " --> pdb=" O   LEU B 947 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   THR B 972 " --> pdb=" O   LEU B 942 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   PHE B 944 " --> pdb=" O   THR B 972 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU B 974 " --> pdb=" O   PHE B 944 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   PHE B 946 " --> pdb=" O   LEU B 974 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 976 " --> pdb=" O   PHE B 946 " (cutoff:3.500A)

    207 hydrogen bonds defined for protein.
    594 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: 2.32

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 5385
        1.04 -     1.23: 242
        1.23 -     1.43: 2090
        1.43 -     1.63: 3293
        1.63 -     1.83: 49
  Bond restraints: 11059
  Sorted by residual:
  bond pdb=" C5  FUC E   3 "
       pdb=" O5  FUC E   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.462 -0.039 2.00e-02 2.50e+03 3.79e+00
  bond pdb=" C1  FUC E   3 "
       pdb=" O5  FUC E   3 "
    ideal  model  delta    sigma   weight residual
    1.400  1.434 -0.034 2.00e-02 2.50e+03 2.90e+00
  bond pdb=" C1  NAG B1101 "
       pdb=" O5  NAG B1101 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.98e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" C   ALA C2670 "
       pdb=" N   PRO C2671 "
    ideal  model  delta    sigma   weight residual
    1.326  1.345 -0.019 1.44e-02 4.82e+03 1.65e+00
  ... (remaining 11054 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 18718
        1.14 -     2.27: 1119
        2.27 -     3.41: 91
        3.41 -     4.55: 18
        4.55 -     5.69: 5
  Bond angle restraints: 19951
  Sorted by residual:
  angle pdb=" CA  CYS A 606 "
        pdb=" C   CYS A 606 "
        pdb=" O   CYS A 606 "
      ideal   model   delta    sigma   weight residual
     119.08  121.59   -2.51 1.03e+00 9.43e-01 5.93e+00
  angle pdb=" CA  ILE C2557 "
        pdb=" CB  ILE C2557 "
        pdb=" CG1 ILE C2557 "
      ideal   model   delta    sigma   weight residual
     110.40  113.90   -3.50 1.70e+00 3.46e-01 4.23e+00
  angle pdb=" C   ILE C2557 "
        pdb=" CA  ILE C2557 "
        pdb=" CB  ILE C2557 "
      ideal   model   delta    sigma   weight residual
     111.53  114.18   -2.65 1.30e+00 5.92e-01 4.16e+00
  angle pdb=" N   ASN C2451 "
        pdb=" CA  ASN C2451 "
        pdb=" C   ASN C2451 "
      ideal   model   delta    sigma   weight residual
     108.19  105.67    2.52 1.29e+00 6.01e-01 3.83e+00
  angle pdb=" N   ILE C2557 "
        pdb=" CA  ILE C2557 "
        pdb=" C   ILE C2557 "
      ideal   model   delta    sigma   weight residual
     106.85  104.08    2.77 1.42e+00 4.96e-01 3.80e+00
  ... (remaining 19946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4627
       17.74 -    35.47: 502
       35.47 -    53.21: 164
       53.21 -    70.94: 43
       70.94 -    88.68: 17
  Dihedral angle restraints: 5353
    sinusoidal: 3009
      harmonic: 2344
  Sorted by residual:
  dihedral pdb=" CB  CYS C2377 "
           pdb=" SG  CYS C2377 "
           pdb=" SG  CYS C2591 "
           pdb=" CB  CYS C2591 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.53  -87.47     1      1.00e+01 1.00e-02 9.18e+01
  dihedral pdb=" CB  CYS C2387 "
           pdb=" SG  CYS C2387 "
           pdb=" SG  CYS B 602 "
           pdb=" CB  CYS B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.05  -61.05     1      1.00e+01 1.00e-02 4.95e+01
  dihedral pdb=" CA  CYS C2591 "
           pdb=" C   CYS C2591 "
           pdb=" N   ASN C2592 "
           pdb=" CA  ASN C2592 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.32  -21.68     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 5350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 812
       0.067 -    0.133: 96
       0.133 -    0.200: 1
       0.200 -    0.267: 0
       0.267 -    0.333: 2
  Chirality restraints: 911
  Sorted by residual:
  chirality pdb=" C1  NAG B1101 "
            pdb=" ND2 ASN B 954 "
            pdb=" C2  NAG B1101 "
            pdb=" O5  NAG B1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN C2558 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 897 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.62e-01
  ... (remaining 908 not shown)

  Planarity restraints: 1678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C2399 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO C2400 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C2400 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C2400 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 588 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO A 589 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 590 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 591 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 591 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 591 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1675 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 847
        2.19 -     2.79: 22444
        2.79 -     3.40: 31069
        3.40 -     4.00: 40349
        4.00 -     4.60: 62109
  Nonbonded interactions: 156818
  Sorted by model distance:
  nonbonded pdb=" O   GLU C2628 "
            pdb="HH21 ARG C2713 "
     model   vdw
     1.589 2.450
  nonbonded pdb=" O   SER C2534 "
            pdb="HH22 ARG C2811 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OE1 GLU C2637 "
            pdb="HD22 ASN C2805 "
     model   vdw
     1.620 2.450
  nonbonded pdb="HH12 ARG C2663 "
            pdb=" O   PRO C2731 "
     model   vdw
     1.635 2.450
  nonbonded pdb=" OD1 ASP C2408 "
            pdb=" HG  SER C2410 "
     model   vdw
     1.639 2.450
  ... (remaining 156813 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 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.42 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:             0.490
  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:             0.070
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.640
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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      :  0.003   0.039   5687  Z= 0.147
  Angle     :  0.605   6.564   7734  Z= 0.300
  Chirality :  0.042   0.333    911
  Planarity :  0.004   0.047   1004
  Dihedral  : 17.790  88.680   2222
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.60 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 26.41 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.32), residues: 700
  helix:  0.61 (0.33), residues: 275
  sheet: -0.50 (0.52), residues: 103
  loop : -2.57 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1013 
 TYR   0.008   0.001   TYR C2391 
 PHE   0.010   0.001   PHE C2418 
 TRP   0.002   0.000   TRP C2602 
 HIS   0.005   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5671)
  covalent geometry    : angle       0.58460 ( 7694)
  SS BOND              : bond        0.00345 (    8)
  SS BOND              : angle       1.13674 (   16)
  hydrogen bonds       : bond        0.15787 (  207)
  hydrogen bonds       : angle       6.75222 (  594)
  link_BETA1-4         : bond        0.00304 (    2)
  link_BETA1-4         : angle       2.94017 (    6)
  link_BETA1-6         : bond        0.00553 (    2)
  link_BETA1-6         : angle       1.67821 (    6)
  link_NAG-ASN         : bond        0.00659 (    4)
  link_NAG-ASN         : angle       3.06215 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.2261
  time to fit residues: 23.7285
Evaluate side-chains
  82 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  954 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C2791 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.154463 restraints weight = 32672.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.93
r_work: 0.3711 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.0664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   5687  Z= 0.179
  Angle     :  0.596   5.011   7734  Z= 0.311
  Chirality :  0.042   0.248    911
  Planarity :  0.005   0.051   1004
  Dihedral  :  6.699  53.966    926
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.60 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.58 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.32), residues: 700
  helix:  0.76 (0.33), residues: 273
  sheet: -0.83 (0.48), residues: 107
  loop : -2.67 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C2814 
 TYR   0.011   0.001   TYR C2450 
 PHE   0.026   0.002   PHE B 882 
 TRP   0.003   0.001   TRP B1017 
 HIS   0.006   0.001   HIS B 896 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 5671)
  covalent geometry    : angle       0.58243 ( 7694)
  SS BOND              : bond        0.00435 (    8)
  SS BOND              : angle       1.22469 (   16)
  hydrogen bonds       : bond        0.04200 (  207)
  hydrogen bonds       : angle       5.23943 (  594)
  link_BETA1-4         : bond        0.00335 (    2)
  link_BETA1-4         : angle       2.18939 (    6)
  link_BETA1-6         : bond        0.00442 (    2)
  link_BETA1-6         : angle       1.43264 (    6)
  link_NAG-ASN         : bond        0.00517 (    4)
  link_NAG-ASN         : angle       2.39509 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6756 (ptp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 96
  average time/residue: 0.2297
  time to fit residues: 27.5249
Evaluate side-chains
  91 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2626 SER
Chi-restraints excluded: chain C residue 2654 ASP
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  901 ILE
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain A residue  598 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153956 restraints weight = 32585.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 3.01
r_work: 0.3715 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5687  Z= 0.126
  Angle     :  0.559   4.917   7734  Z= 0.288
  Chirality :  0.041   0.222    911
  Planarity :  0.004   0.049   1004
  Dihedral  :  6.341  54.592    926
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.31 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.25 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.32), residues: 700
  helix:  0.91 (0.33), residues: 274
  sheet: -1.19 (0.48), residues: 109
  loop : -2.55 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C2811 
 TYR   0.010   0.001   TYR C2450 
 PHE   0.013   0.001   PHE B 882 
 TRP   0.002   0.000   TRP B1017 
 HIS   0.009   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5671)
  covalent geometry    : angle       0.54675 ( 7694)
  SS BOND              : bond        0.00353 (    8)
  SS BOND              : angle       0.98485 (   16)
  hydrogen bonds       : bond        0.03773 (  207)
  hydrogen bonds       : angle       4.85314 (  594)
  link_BETA1-4         : bond        0.00226 (    2)
  link_BETA1-4         : angle       2.14390 (    6)
  link_BETA1-6         : bond        0.00400 (    2)
  link_BETA1-6         : angle       1.27013 (    6)
  link_NAG-ASN         : bond        0.00525 (    4)
  link_NAG-ASN         : angle       2.38099 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.6958 (ttp-170) cc_final: 0.6712 (ptp-170)
  outliers start: 10
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2600
  time to fit residues: 29.9492
Evaluate side-chains
  92 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.178834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.152797 restraints weight = 32588.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.98
r_work: 0.3718 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5687  Z= 0.145
  Angle     :  0.566   4.845   7734  Z= 0.291
  Chirality :  0.041   0.219    911
  Planarity :  0.004   0.051   1004
  Dihedral  :  6.305  54.523    926
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.89 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.42 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.32), residues: 700
  helix:  0.89 (0.32), residues: 275
  sheet: -1.28 (0.48), residues: 109
  loop : -2.63 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C2811 
 TYR   0.011   0.001   TYR C2450 
 PHE   0.019   0.001   PHE B 882 
 TRP   0.002   0.001   TRP B1017 
 HIS   0.005   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5671)
  covalent geometry    : angle       0.55359 ( 7694)
  SS BOND              : bond        0.00378 (    8)
  SS BOND              : angle       1.06392 (   16)
  hydrogen bonds       : bond        0.03500 (  207)
  hydrogen bonds       : angle       4.74032 (  594)
  link_BETA1-4         : bond        0.00102 (    2)
  link_BETA1-4         : angle       1.99430 (    6)
  link_BETA1-6         : bond        0.00381 (    2)
  link_BETA1-6         : angle       1.30174 (    6)
  link_NAG-ASN         : bond        0.00484 (    4)
  link_NAG-ASN         : angle       2.40116 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6825 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7642 (mp)
REVERT: C 2608 ASP cc_start: 0.7281 (m-30) cc_final: 0.7066 (m-30)
REVERT: A  603 MET cc_start: 0.6251 (mmm) cc_final: 0.5949 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 98
  average time/residue: 0.2132
  time to fit residues: 26.1257
Evaluate side-chains
  95 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.178836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.152647 restraints weight = 30960.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 3.01
r_work: 0.3724 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5687  Z= 0.141
  Angle     :  0.593  12.951   7734  Z= 0.303
  Chirality :  0.040   0.220    911
  Planarity :  0.004   0.051   1004
  Dihedral  :  6.331  53.548    926
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.46 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 24.09 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.32), residues: 700
  helix:  0.93 (0.32), residues: 275
  sheet: -1.35 (0.48), residues: 109
  loop : -2.60 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2811 
 TYR   0.010   0.001   TYR C2450 
 PHE   0.016   0.001   PHE B 882 
 TRP   0.002   0.000   TRP B1017 
 HIS   0.004   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5671)
  covalent geometry    : angle       0.55680 ( 7694)
  SS BOND              : bond        0.00305 (    8)
  SS BOND              : angle       3.80144 (   16)
  hydrogen bonds       : bond        0.03492 (  207)
  hydrogen bonds       : angle       4.65483 (  594)
  link_BETA1-4         : bond        0.00174 (    2)
  link_BETA1-4         : angle       1.96589 (    6)
  link_BETA1-6         : bond        0.00390 (    2)
  link_BETA1-6         : angle       1.31046 (    6)
  link_NAG-ASN         : bond        0.00493 (    4)
  link_NAG-ASN         : angle       2.44170 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7142 (ttp-170) cc_final: 0.6850 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7600 (mp)
REVERT: C 2608 ASP cc_start: 0.7289 (m-30) cc_final: 0.7065 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 98
  average time/residue: 0.2147
  time to fit residues: 26.1733
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  901 ILE
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.179938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.155085 restraints weight = 31974.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 2.87
r_work: 0.3726 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5687  Z= 0.137
  Angle     :  0.574   8.515   7734  Z= 0.294
  Chirality :  0.040   0.218    911
  Planarity :  0.004   0.052   1004
  Dihedral  :  6.250  52.443    926
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.60 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.09 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.32), residues: 700
  helix:  1.00 (0.32), residues: 275
  sheet: -1.38 (0.48), residues: 109
  loop : -2.63 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2509 
 TYR   0.010   0.001   TYR C2450 
 PHE   0.016   0.001   PHE B 882 
 TRP   0.002   0.000   TRP B1017 
 HIS   0.009   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5671)
  covalent geometry    : angle       0.55147 ( 7694)
  SS BOND              : bond        0.00419 (    8)
  SS BOND              : angle       2.55451 (   16)
  hydrogen bonds       : bond        0.03367 (  207)
  hydrogen bonds       : angle       4.57674 (  594)
  link_BETA1-4         : bond        0.00211 (    2)
  link_BETA1-4         : angle       1.88457 (    6)
  link_BETA1-6         : bond        0.00406 (    2)
  link_BETA1-6         : angle       1.30536 (    6)
  link_NAG-ASN         : bond        0.00476 (    4)
  link_NAG-ASN         : angle       2.47343 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7151 (ttp-170) cc_final: 0.6829 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: C 2608 ASP cc_start: 0.7279 (m-30) cc_final: 0.7059 (m-30)
  outliers start: 16
  outliers final: 15
  residues processed: 95
  average time/residue: 0.2262
  time to fit residues: 26.6160
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  880 LEU
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  901 ILE
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C2791 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153701 restraints weight = 30473.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.97
r_work: 0.3724 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5687  Z= 0.136
  Angle     :  0.570   5.843   7734  Z= 0.292
  Chirality :  0.040   0.219    911
  Planarity :  0.004   0.052   1004
  Dihedral  :  6.231  51.261    926
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.74 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.09 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.32), residues: 700
  helix:  1.06 (0.33), residues: 274
  sheet: -1.43 (0.48), residues: 110
  loop : -2.61 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1013 
 TYR   0.010   0.001   TYR C2450 
 PHE   0.016   0.001   PHE B 882 
 TRP   0.001   0.000   TRP B1017 
 HIS   0.007   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 5671)
  covalent geometry    : angle       0.55270 ( 7694)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.89811 (   16)
  hydrogen bonds       : bond        0.03357 (  207)
  hydrogen bonds       : angle       4.54029 (  594)
  link_BETA1-4         : bond        0.00241 (    2)
  link_BETA1-4         : angle       1.87040 (    6)
  link_BETA1-6         : bond        0.00359 (    2)
  link_BETA1-6         : angle       1.28906 (    6)
  link_NAG-ASN         : bond        0.00490 (    4)
  link_NAG-ASN         : angle       2.47573 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7046 (ttp-170) cc_final: 0.6724 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: C 2608 ASP cc_start: 0.7298 (m-30) cc_final: 0.7074 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1768
  time to fit residues: 21.4361
Evaluate side-chains
  95 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  880 LEU
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  901 ILE
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C2791 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.154141 restraints weight = 29328.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.88
r_work: 0.3716 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5687  Z= 0.135
  Angle     :  0.569   5.537   7734  Z= 0.292
  Chirality :  0.040   0.217    911
  Planarity :  0.004   0.052   1004
  Dihedral  :  6.189  50.264    926
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.17 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.59 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.32), residues: 700
  helix:  1.06 (0.32), residues: 275
  sheet: -1.45 (0.48), residues: 110
  loop : -2.59 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1013 
 TYR   0.010   0.001   TYR C2450 
 PHE   0.015   0.001   PHE B 882 
 TRP   0.002   0.000   TRP B1017 
 HIS   0.007   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5671)
  covalent geometry    : angle       0.55244 ( 7694)
  SS BOND              : bond        0.00373 (    8)
  SS BOND              : angle       1.72819 (   16)
  hydrogen bonds       : bond        0.03306 (  207)
  hydrogen bonds       : angle       4.50168 (  594)
  link_BETA1-4         : bond        0.00233 (    2)
  link_BETA1-4         : angle       1.81319 (    6)
  link_BETA1-6         : bond        0.00398 (    2)
  link_BETA1-6         : angle       1.29767 (    6)
  link_NAG-ASN         : bond        0.00468 (    4)
  link_NAG-ASN         : angle       2.51142 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7039 (ttp-170) cc_final: 0.6736 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: C 2608 ASP cc_start: 0.7330 (m-30) cc_final: 0.7106 (m-30)
  outliers start: 16
  outliers final: 15
  residues processed: 93
  average time/residue: 0.1777
  time to fit residues: 21.1957
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  880 LEU
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  901 ILE
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    0.2980
   chunk 68 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.179304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.154641 restraints weight = 31189.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 2.84
r_work: 0.3742 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5687  Z= 0.123
  Angle     :  0.562   5.656   7734  Z= 0.288
  Chirality :  0.040   0.217    911
  Planarity :  0.004   0.051   1004
  Dihedral  :  6.119  49.144    926
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.46 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 23.42 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.33), residues: 700
  helix:  1.13 (0.33), residues: 275
  sheet: -1.45 (0.48), residues: 110
  loop : -2.52 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1013 
 TYR   0.009   0.001   TYR C2450 
 PHE   0.014   0.001   PHE B 882 
 TRP   0.001   0.000   TRP B1017 
 HIS   0.007   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5671)
  covalent geometry    : angle       0.54645 ( 7694)
  SS BOND              : bond        0.00352 (    8)
  SS BOND              : angle       1.57684 (   16)
  hydrogen bonds       : bond        0.03223 (  207)
  hydrogen bonds       : angle       4.45360 (  594)
  link_BETA1-4         : bond        0.00296 (    2)
  link_BETA1-4         : angle       1.82416 (    6)
  link_BETA1-6         : bond        0.00423 (    2)
  link_BETA1-6         : angle       1.29025 (    6)
  link_NAG-ASN         : bond        0.00493 (    4)
  link_NAG-ASN         : angle       2.47669 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.6958 (ttp-170) cc_final: 0.6678 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7736 (mp)
REVERT: C 2608 ASP cc_start: 0.7407 (m-30) cc_final: 0.7180 (m-30)
REVERT: C 2706 MET cc_start: 0.8572 (mmt) cc_final: 0.8216 (mmt)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1972
  time to fit residues: 23.6440
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2481 THR
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2626 SER
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  604 CYS
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  880 LEU
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0670
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.180231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.153835 restraints weight = 35147.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 3.16
r_work: 0.3704 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5687  Z= 0.116
  Angle     :  0.559   5.802   7734  Z= 0.286
  Chirality :  0.040   0.214    911
  Planarity :  0.004   0.049   1004
  Dihedral  :  6.045  49.119    926
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.03 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 23.75 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.33), residues: 700
  helix:  1.18 (0.33), residues: 275
  sheet: -1.45 (0.48), residues: 110
  loop : -2.51 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1013 
 TYR   0.008   0.001   TYR C2450 
 PHE   0.013   0.001   PHE C2819 
 TRP   0.001   0.000   TRP B1017 
 HIS   0.007   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5671)
  covalent geometry    : angle       0.54345 ( 7694)
  SS BOND              : bond        0.00277 (    8)
  SS BOND              : angle       1.56027 (   16)
  hydrogen bonds       : bond        0.03174 (  207)
  hydrogen bonds       : angle       4.41645 (  594)
  link_BETA1-4         : bond        0.00306 (    2)
  link_BETA1-4         : angle       1.79749 (    6)
  link_BETA1-6         : bond        0.00413 (    2)
  link_BETA1-6         : angle       1.27389 (    6)
  link_NAG-ASN         : bond        0.00489 (    4)
  link_NAG-ASN         : angle       2.46629 (   12)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  597 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 2370 ARG cc_start: 0.7072 (ttp-170) cc_final: 0.6798 (ptp-170)
REVERT: C 2555 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7724 (mp)
REVERT: C 2608 ASP cc_start: 0.7444 (m-30) cc_final: 0.7215 (m-30)
REVERT: C 2706 MET cc_start: 0.8509 (mmt) cc_final: 0.8158 (mmt)
  outliers start: 14
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1657
  time to fit residues: 19.9384
Evaluate side-chains
  94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2538 ILE
Chi-restraints excluded: chain C residue 2539 THR
Chi-restraints excluded: chain C residue 2555 LEU
Chi-restraints excluded: chain C residue 2626 SER
Chi-restraints excluded: chain C residue 2683 VAL
Chi-restraints excluded: chain C residue 2752 LEU
Chi-restraints excluded: chain C residue 2756 GLN
Chi-restraints excluded: chain B residue  833 ASP
Chi-restraints excluded: chain B residue  880 LEU
Chi-restraints excluded: chain B residue  897 ASN
Chi-restraints excluded: chain B residue  954 ASN
Chi-restraints excluded: chain B residue 1007 GLN
Chi-restraints excluded: chain A residue  605 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C2669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.179659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.154051 restraints weight = 29678.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.93
r_work: 0.3733 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5687  Z= 0.126
  Angle     :  0.562   5.765   7734  Z= 0.289
  Chirality :  0.040   0.216    911
  Planarity :  0.004   0.050   1004
  Dihedral  :  6.046  49.575    926
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.03 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 23.75 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.32), residues: 700
  helix:  1.18 (0.33), residues: 275
  sheet: -1.44 (0.48), residues: 110
  loop : -2.53 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1013 
 TYR   0.009   0.001   TYR C2450 
 PHE   0.014   0.001   PHE B 882 
 TRP   0.002   0.000   TRP B1017 
 HIS   0.007   0.001   HIS C2669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5671)
  covalent geometry    : angle       0.54699 ( 7694)
  SS BOND              : bond        0.00303 (    8)
  SS BOND              : angle       1.56617 (   16)
  hydrogen bonds       : bond        0.03180 (  207)
  hydrogen bonds       : angle       4.42690 (  594)
  link_BETA1-4         : bond        0.00321 (    2)
  link_BETA1-4         : angle       1.74001 (    6)
  link_BETA1-6         : bond        0.00386 (    2)
  link_BETA1-6         : angle       1.28657 (    6)
  link_NAG-ASN         : bond        0.00471 (    4)
  link_NAG-ASN         : angle       2.44195 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2812.86 seconds
wall clock time: 48 minutes 18.56 seconds (2898.56 seconds total)