Starting phenix.real_space_refine
on Sat Aug 23 03:30:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t6u_41081/08_2025/8t6u_41081.map"
  }
  resolution = 3.13
  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=  -0.003 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    5826      2.51       5
     N    1328      2.21       5
     O    1446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8638
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4071
          Classifications: {'peptide': 516}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 4071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4071
          Classifications: {'peptide': 516}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 256
          Unusual residues: {'CLR': 4, 'H9F': 1, 'PC1': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 148
          Unusual residues: {'CLR': 4, 'H9F': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 2.10, per 1000 atoms: 0.24
  Number of scatterers: 8638
  At special positions: 0
  Unit cell: (72.092, 132.348, 83.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       2     15.00
     O    1446      8.00
     N    1328      7.00
     C    5826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG L   1 " - " NAG L   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 642 "
      " NAG L   1 " - " ASN B 642 "
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 196.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      73.3% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
      removed outlier: 3.515A  pdb=" N   VAL A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 402 through 431
      removed outlier: 3.709A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 3.521A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 547
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.580A  pdb=" N   LEU A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
    Processing helix  chain 'A' and resid 608 through 624
      removed outlier: 3.535A  pdb=" N   ILE A 612 " --> pdb=" O   PHE A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
    Processing helix  chain 'A' and resid 667 through 690
    Processing helix  chain 'A' and resid 701 through 717
      removed outlier: 3.692A  pdb=" N   ASP A 705 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 706 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 720
      No H-bonds generated for 'chain 'A' and resid 718 through 720'
    Processing helix  chain 'A' and resid 727 through 738
    Processing helix  chain 'A' and resid 760 through 772
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.974A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 812
    Processing helix  chain 'A' and resid 822 through 828
    Processing helix  chain 'A' and resid 829 through 853
    Processing helix  chain 'A' and resid 858 through 865
      removed outlier: 3.553A  pdb=" N   LEU A 865 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 873
      removed outlier: 3.534A  pdb=" N   ARG A 870 " --> pdb=" O   THR A 866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.821A  pdb=" N   ILE A 877 " --> pdb=" O   LEU A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 887
    Processing helix  chain 'B' and resid 379 through 390
      removed outlier: 3.513A  pdb=" N   VAL B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 402 through 431
      removed outlier: 3.706A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 3.520A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 507 " --> pdb=" O   LEU B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 515
    Processing helix  chain 'B' and resid 517 through 547
    Processing helix  chain 'B' and resid 569 through 593
      removed outlier: 3.581A  pdb=" N   LEU B 573 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 608
    Processing helix  chain 'B' and resid 608 through 624
      removed outlier: 3.536A  pdb=" N   ILE B 612 " --> pdb=" O   PHE B 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
    Processing helix  chain 'B' and resid 667 through 690
    Processing helix  chain 'B' and resid 701 through 717
      removed outlier: 3.690A  pdb=" N   ASP B 705 " --> pdb=" O   GLY B 701 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU B 706 " --> pdb=" O   PHE B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 720
      No H-bonds generated for 'chain 'B' and resid 718 through 720'
    Processing helix  chain 'B' and resid 727 through 738
    Processing helix  chain 'B' and resid 760 through 772
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.974A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 812
    Processing helix  chain 'B' and resid 822 through 828
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 858 through 865
      removed outlier: 3.554A  pdb=" N   LEU B 865 " --> pdb=" O   PHE B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 873
      removed outlier: 3.533A  pdb=" N   ARG B 870 " --> pdb=" O   THR B 866 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 878
      removed outlier: 3.827A  pdb=" N   ILE B 877 " --> pdb=" O   LEU B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742
      removed outlier: 7.366A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A 754 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN A 752 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742
      removed outlier: 7.365A  pdb=" N   VAL B 740 " --> pdb=" O   GLN B 754 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN B 754 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN B 752 " --> pdb=" O   GLY B 742 " (cutoff:3.500A)

    518 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1333
        1.32 -     1.45: 2348
        1.45 -     1.58: 5084
        1.58 -     1.71: 5
        1.71 -     1.84: 66
  Bond restraints: 8836
  Sorted by residual:
  bond pdb=" C5  H9F B2203 "
       pdb=" N8  H9F B2203 "
    ideal  model  delta    sigma   weight residual
    1.348  1.508 -0.160 2.00e-02 2.50e+03 6.37e+01
  bond pdb=" C5  H9F A2204 "
       pdb=" N8  H9F A2204 "
    ideal  model  delta    sigma   weight residual
    1.348  1.487 -0.139 2.00e-02 2.50e+03 4.86e+01
  bond pdb=" C2  H9F B2203 "
       pdb=" N7  H9F B2203 "
    ideal  model  delta    sigma   weight residual
    1.360  1.490 -0.130 2.00e-02 2.50e+03 4.24e+01
  bond pdb=" C2  H9F A2204 "
       pdb=" N7  H9F A2204 "
    ideal  model  delta    sigma   weight residual
    1.360  1.482 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" C6  H9F B2203 "
       pdb=" N6  H9F B2203 "
    ideal  model  delta    sigma   weight residual
    1.364  1.471 -0.107 2.00e-02 2.50e+03 2.86e+01
  ... (remaining 8831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8760
        1.47 -     2.93: 2470
        2.93 -     4.40: 733
        4.40 -     5.86: 64
        5.86 -     7.33: 9
  Bond angle restraints: 12036
  Sorted by residual:
  angle pdb=" C   ILE B 493 "
        pdb=" N   GLY B 494 "
        pdb=" CA  GLY B 494 "
      ideal   model   delta    sigma   weight residual
     119.98  125.48   -5.50 1.11e+00 8.12e-01 2.45e+01
  angle pdb=" C   ILE A 493 "
        pdb=" N   GLY A 494 "
        pdb=" CA  GLY A 494 "
      ideal   model   delta    sigma   weight residual
     119.98  125.42   -5.44 1.11e+00 8.12e-01 2.41e+01
  angle pdb=" N   GLN A 434 "
        pdb=" CA  GLN A 434 "
        pdb=" C   GLN A 434 "
      ideal   model   delta    sigma   weight residual
     111.28  106.09    5.19 1.09e+00 8.42e-01 2.27e+01
  angle pdb=" N   PRO A 722 "
        pdb=" CA  PRO A 722 "
        pdb=" C   PRO A 722 "
      ideal   model   delta    sigma   weight residual
     110.55  117.88   -7.33 1.63e+00 3.76e-01 2.02e+01
  angle pdb=" N   PRO B 722 "
        pdb=" CA  PRO B 722 "
        pdb=" C   PRO B 722 "
      ideal   model   delta    sigma   weight residual
     110.55  117.72   -7.17 1.63e+00 3.76e-01 1.94e+01
  ... (remaining 12031 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.06: 5507
       34.06 -    68.12: 167
       68.12 -   102.18: 16
      102.18 -   136.24: 3
      136.24 -   170.30: 1
  Dihedral angle restraints: 5694
    sinusoidal: 2718
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" C18 H9F A2204 "
           pdb=" C19 H9F A2204 "
           pdb=" N7  H9F A2204 "
           pdb=" C2  H9F A2204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.87  -98.83 -170.30     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C17 H9F A2204 "
           pdb=" C18 H9F A2204 "
           pdb=" C19 H9F A2204 "
           pdb=" N7  H9F A2204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.70  -69.79  125.49     1      3.00e+01 1.11e-03 1.69e+01
  dihedral pdb=" C21 H9F B2203 "
           pdb=" C22 H9F B2203 "
           pdb=" C23 H9F B2203 "
           pdb=" C24 H9F B2203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.51   52.53 -117.04     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.848: 1434
       0.848 -    1.697: 0
       1.697 -    2.545: 0
       2.545 -    3.393: 0
       3.393 -    4.241: 2
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    1.84   -4.24 2.00e-02 2.50e+03 4.50e+04
  chirality pdb=" C1  NAG L   2 "
            pdb=" O4  NAG L   1 "
            pdb=" C2  NAG L   2 "
            pdb=" O5  NAG L   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    1.83   -4.23 2.00e-02 2.50e+03 4.48e+04
  chirality pdb=" CB  ILE A 493 "
            pdb=" CA  ILE A 493 "
            pdb=" CG1 ILE A 493 "
            pdb=" CG2 ILE A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1433 not shown)

  Planarity restraints: 1406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.072 2.00e-02 2.50e+03   6.31e-02 4.98e+01
        pdb=" C7  NAG D   1 "   -0.056 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.065 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.085 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG L   1 "   -0.068 2.00e-02 2.50e+03   5.99e-02 4.48e+01
        pdb=" C7  NAG L   1 "    0.054 2.00e-02 2.50e+03
        pdb=" C8  NAG L   1 "   -0.062 2.00e-02 2.50e+03
        pdb=" N2  NAG L   1 "    0.081 2.00e-02 2.50e+03
        pdb=" O7  NAG L   1 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 878 "   -0.042 2.00e-02 2.50e+03   3.28e-02 1.88e+01
        pdb=" CG  PHE A 878 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 878 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 878 "    0.053 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 878 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 878 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 878 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1403 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 895
        2.78 -     3.31: 9182
        3.31 -     3.84: 14079
        3.84 -     4.37: 18538
        4.37 -     4.90: 30013
  Nonbonded interactions: 72707
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 555 "
            pdb=" OH  TYR B 555 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NH2 ARG A 646 "
            pdb=" CA  GLY A 720 "
     model   vdw
     2.373 3.520
  nonbonded pdb=" NH2 ARG A 879 "
            pdb=" OE2 GLU A 882 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" NH2 ARG B 879 "
            pdb=" OE2 GLU B 882 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" OG1 THR B 739 "
            pdb=" O   HOH B2301 "
     model   vdw
     2.449 3.040
  ... (remaining 72702 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 369 through 2202 or resid 2205))
  selection = (chain 'B' and (resid 369 through 2202 or resid 2205))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.470
  Find NCS groups from input model:        0.100
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.160   8840  Z= 0.708
  Angle     :  1.533  27.809  12048  Z= 1.032
  Chirality :  0.175   4.241   1436
  Planarity :  0.009   0.096   1404
  Dihedral  : 15.188 170.302   3774
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.64 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.02 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.20), residues: 1024
  helix: -1.70 (0.15), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.66 (0.27), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.003   ARG B 389 
 TYR   0.036   0.009   TYR A 596 
 PHE   0.053   0.007   PHE A 878 
 TRP   0.036   0.009   TRP B 723 
 HIS   0.018   0.006   HIS B 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.01129 ( 8836)
  covalent geometry    : angle       1.48528 (12036)
  hydrogen bonds       : bond        0.22884 (  518)
  hydrogen bonds       : angle       8.61015 ( 1518)
  link_BETA1-4         : bond        0.06733 (    2)
  link_BETA1-4         : angle      16.96308 (    6)
  link_NAG-ASN         : bond        0.00476 (    2)
  link_NAG-ASN         : angle       2.84904 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 LEU cc_start: 0.9412 (tt) cc_final: 0.9208 (tp)
REVERT: A  554 ASN cc_start: 0.8690 (t0) cc_final: 0.8470 (t0)
REVERT: B  406 LEU cc_start: 0.9404 (tt) cc_final: 0.9197 (tp)
REVERT: B  554 ASN cc_start: 0.8692 (t0) cc_final: 0.8476 (t0)
REVERT: B  712 MET cc_start: 0.8731 (mtm) cc_final: 0.8526 (mtm)
  outliers start: 3
  outliers final: 3
  residues processed: 135
  average time/residue: 0.0869
  time to fit residues: 15.8414
Evaluate side-chains
  65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain B residue  740 VAL
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.072243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.061068 restraints weight = 25189.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.01
r_work: 0.2840 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8840  Z= 0.149
  Angle     :  0.605   6.876  12048  Z= 0.300
  Chirality :  0.039   0.133   1436
  Planarity :  0.005   0.046   1404
  Dihedral  : 12.277 149.184   1877
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.93 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.26), residues: 1024
  helix:  1.08 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -1.59 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 879 
 TYR   0.009   0.002   TYR B 818 
 PHE   0.026   0.002   PHE A 411 
 TRP   0.018   0.002   TRP B 831 
 HIS   0.003   0.001   HIS B 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8836)
  covalent geometry    : angle       0.60337 (12036)
  hydrogen bonds       : bond        0.04445 (  518)
  hydrogen bonds       : angle       4.74540 ( 1518)
  link_BETA1-4         : bond        0.00432 (    2)
  link_BETA1-4         : angle       1.73817 (    6)
  link_NAG-ASN         : bond        0.00130 (    2)
  link_NAG-ASN         : angle       1.34642 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  406 LEU cc_start: 0.9064 (tt) cc_final: 0.8858 (tp)
REVERT: A  554 ASN cc_start: 0.8438 (t0) cc_final: 0.8115 (t0)
REVERT: A  721 MET cc_start: 0.8882 (mpp) cc_final: 0.8660 (mpp)
REVERT: B  406 LEU cc_start: 0.9030 (tt) cc_final: 0.8819 (tp)
REVERT: B  554 ASN cc_start: 0.8426 (t0) cc_final: 0.8103 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0736
  time to fit residues: 8.1452
Evaluate side-chains
  67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  697 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  873 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 95 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.071852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.060962 restraints weight = 25018.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.93
r_work: 0.2840 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8840  Z= 0.135
  Angle     :  0.544   7.558  12048  Z= 0.266
  Chirality :  0.039   0.150   1436
  Planarity :  0.005   0.050   1404
  Dihedral  : 11.375 138.057   1875
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.05 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.26), residues: 1024
  helix:  1.72 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -1.25 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 879 
 TYR   0.017   0.001   TYR B 818 
 PHE   0.014   0.001   PHE A 411 
 TRP   0.013   0.001   TRP B 831 
 HIS   0.002   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8836)
  covalent geometry    : angle       0.54357 (12036)
  hydrogen bonds       : bond        0.03895 (  518)
  hydrogen bonds       : angle       4.28154 ( 1518)
  link_BETA1-4         : bond        0.00403 (    2)
  link_BETA1-4         : angle       1.31717 (    6)
  link_NAG-ASN         : bond        0.00126 (    2)
  link_NAG-ASN         : angle       0.94021 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  406 LEU cc_start: 0.9121 (tt) cc_final: 0.8902 (tp)
REVERT: A  554 ASN cc_start: 0.8385 (t0) cc_final: 0.8079 (t0)
REVERT: B  406 LEU cc_start: 0.9094 (tt) cc_final: 0.8880 (tp)
REVERT: B  554 ASN cc_start: 0.8375 (t0) cc_final: 0.8073 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0623
  time to fit residues: 6.5012
Evaluate side-chains
  64 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  697 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.071875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.060879 restraints weight = 25764.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 3.00
r_work: 0.2837 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8840  Z= 0.128
  Angle     :  0.521   5.817  12048  Z= 0.254
  Chirality :  0.038   0.140   1436
  Planarity :  0.005   0.051   1404
  Dihedral  : 10.570 128.724   1875
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.60 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.26), residues: 1024
  helix:  1.84 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -1.04 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 656 
 TYR   0.018   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 411 
 TRP   0.012   0.001   TRP B 831 
 HIS   0.002   0.001   HIS B 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8836)
  covalent geometry    : angle       0.52010 (12036)
  hydrogen bonds       : bond        0.03717 (  518)
  hydrogen bonds       : angle       4.12651 ( 1518)
  link_BETA1-4         : bond        0.00376 (    2)
  link_BETA1-4         : angle       0.77068 (    6)
  link_NAG-ASN         : bond        0.00065 (    2)
  link_NAG-ASN         : angle       1.01380 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  406 LEU cc_start: 0.9118 (tt) cc_final: 0.8902 (tp)
REVERT: A  554 ASN cc_start: 0.8371 (t0) cc_final: 0.8083 (t0)
REVERT: B  406 LEU cc_start: 0.9102 (tt) cc_final: 0.8881 (tp)
REVERT: B  554 ASN cc_start: 0.8366 (t0) cc_final: 0.8083 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 67
  average time/residue: 0.0657
  time to fit residues: 6.6332
Evaluate side-chains
  63 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  877 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 70 optimal weight:    0.4980
   chunk 59 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:
B 447 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.071837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.060966 restraints weight = 25703.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.96
r_work: 0.2837 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8840  Z= 0.118
  Angle     :  0.516   6.554  12048  Z= 0.251
  Chirality :  0.038   0.136   1436
  Planarity :  0.005   0.050   1404
  Dihedral  : 10.060 117.418   1875
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.27 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.26), residues: 1024
  helix:  1.91 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.91 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 656 
 TYR   0.014   0.001   TYR B 824 
 PHE   0.012   0.001   PHE B 411 
 TRP   0.010   0.001   TRP B 492 
 HIS   0.001   0.000   HIS B 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8836)
  covalent geometry    : angle       0.51500 (12036)
  hydrogen bonds       : bond        0.03633 (  518)
  hydrogen bonds       : angle       4.00811 ( 1518)
  link_BETA1-4         : bond        0.00381 (    2)
  link_BETA1-4         : angle       0.74985 (    6)
  link_NAG-ASN         : bond        0.00122 (    2)
  link_NAG-ASN         : angle       1.02907 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  406 LEU cc_start: 0.9156 (tt) cc_final: 0.8949 (tp)
REVERT: A  554 ASN cc_start: 0.8360 (t0) cc_final: 0.8086 (t0)
REVERT: B  406 LEU cc_start: 0.9140 (tt) cc_final: 0.8938 (tp)
REVERT: B  554 ASN cc_start: 0.8355 (t0) cc_final: 0.8087 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0730
  time to fit residues: 7.5914
Evaluate side-chains
  65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 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:
A 447 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.071741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.060861 restraints weight = 25547.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.98
r_work: 0.2833 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8840  Z= 0.121
  Angle     :  0.527   6.751  12048  Z= 0.253
  Chirality :  0.038   0.136   1436
  Planarity :  0.005   0.049   1404
  Dihedral  :  9.342  89.358   1874
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.27 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.26), residues: 1024
  helix:  1.98 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.81 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 603 
 TYR   0.015   0.001   TYR A 824 
 PHE   0.012   0.001   PHE A 411 
 TRP   0.010   0.001   TRP A 492 
 HIS   0.001   0.000   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8836)
  covalent geometry    : angle       0.52666 (12036)
  hydrogen bonds       : bond        0.03589 (  518)
  hydrogen bonds       : angle       3.98675 ( 1518)
  link_BETA1-4         : bond        0.00187 (    2)
  link_BETA1-4         : angle       0.59502 (    6)
  link_NAG-ASN         : bond        0.00062 (    2)
  link_NAG-ASN         : angle       1.05983 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  406 LEU cc_start: 0.9183 (tt) cc_final: 0.8972 (tp)
REVERT: A  554 ASN cc_start: 0.8349 (t0) cc_final: 0.8086 (t0)
REVERT: B  406 LEU cc_start: 0.9148 (tt) cc_final: 0.8937 (tp)
REVERT: B  554 ASN cc_start: 0.8355 (t0) cc_final: 0.8096 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 69
  average time/residue: 0.0742
  time to fit residues: 7.7072
Evaluate side-chains
  71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0870
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.071805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.061005 restraints weight = 25532.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.94
r_work: 0.2838 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8840  Z= 0.120
  Angle     :  0.530   7.520  12048  Z= 0.254
  Chirality :  0.038   0.153   1436
  Planarity :  0.005   0.049   1404
  Dihedral  :  9.061  87.175   1874
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.27 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.27), residues: 1024
  helix:  2.01 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.71 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 603 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.011   0.001   PHE B 411 
 TRP   0.009   0.001   TRP A 492 
 HIS   0.001   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8836)
  covalent geometry    : angle       0.52987 (12036)
  hydrogen bonds       : bond        0.03578 (  518)
  hydrogen bonds       : angle       3.96901 ( 1518)
  link_BETA1-4         : bond        0.00355 (    2)
  link_BETA1-4         : angle       0.72772 (    6)
  link_NAG-ASN         : bond        0.00058 (    2)
  link_NAG-ASN         : angle       1.08063 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  435 MET cc_start: 0.9023 (mtp) cc_final: 0.8792 (ttt)
REVERT: A  554 ASN cc_start: 0.8364 (t0) cc_final: 0.7894 (t0)
REVERT: A  721 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7861 (mpp)
REVERT: B  406 LEU cc_start: 0.9158 (tt) cc_final: 0.8949 (tp)
REVERT: B  554 ASN cc_start: 0.8363 (t0) cc_final: 0.7897 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 70
  average time/residue: 0.0768
  time to fit residues: 8.1038
Evaluate side-chains
  71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0170
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7020

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.072023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.061183 restraints weight = 25447.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.96
r_work: 0.2838 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8840  Z= 0.125
  Angle     :  0.544   8.060  12048  Z= 0.259
  Chirality :  0.039   0.278   1436
  Planarity :  0.004   0.050   1404
  Dihedral  :  8.930  87.049   1874
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.72 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.27), residues: 1024
  helix:  1.95 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.60 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.010   0.001   PHE A 411 
 TRP   0.009   0.001   TRP B 492 
 HIS   0.001   0.000   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8836)
  covalent geometry    : angle       0.54324 (12036)
  hydrogen bonds       : bond        0.03610 (  518)
  hydrogen bonds       : angle       4.00554 ( 1518)
  link_BETA1-4         : bond        0.00347 (    2)
  link_BETA1-4         : angle       0.75622 (    6)
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       1.08839 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  554 ASN cc_start: 0.8362 (t0) cc_final: 0.7897 (t0)
REVERT: A  721 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7902 (mpp)
REVERT: B  554 ASN cc_start: 0.8353 (t0) cc_final: 0.7895 (t0)
  outliers start: 18
  outliers final: 16
  residues processed: 66
  average time/residue: 0.0733
  time to fit residues: 7.2907
Evaluate side-chains
  71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.8762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.071236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.060483 restraints weight = 25449.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.93
r_work: 0.2827 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8840  Z= 0.138
  Angle     :  0.574   8.755  12048  Z= 0.270
  Chirality :  0.040   0.275   1436
  Planarity :  0.005   0.050   1404
  Dihedral  :  8.780  86.735   1874
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.05 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.27), residues: 1024
  helix:  1.89 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.50 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 603 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.009   0.001   PHE A 411 
 TRP   0.010   0.001   TRP B 831 
 HIS   0.001   0.001   HIS B 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8836)
  covalent geometry    : angle       0.57313 (12036)
  hydrogen bonds       : bond        0.03684 (  518)
  hydrogen bonds       : angle       4.05467 ( 1518)
  link_BETA1-4         : bond        0.00259 (    2)
  link_BETA1-4         : angle       0.78203 (    6)
  link_NAG-ASN         : bond        0.00041 (    2)
  link_NAG-ASN         : angle       1.10532 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  554 ASN cc_start: 0.8371 (t0) cc_final: 0.7913 (t0)
REVERT: A  603 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8127 (mtm-85)
REVERT: B  554 ASN cc_start: 0.8366 (t0) cc_final: 0.7912 (t0)
  outliers start: 17
  outliers final: 16
  residues processed: 67
  average time/residue: 0.0661
  time to fit residues: 6.7101
Evaluate side-chains
  71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0770
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0980
   overall best weight:    0.4940

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.072071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.061250 restraints weight = 25441.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.94
r_work: 0.2849 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8840  Z= 0.113
  Angle     :  0.552   8.884  12048  Z= 0.259
  Chirality :  0.039   0.303   1436
  Planarity :  0.005   0.049   1404
  Dihedral  :  8.571  87.056   1874
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.05 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.27), residues: 1024
  helix:  2.08 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -0.12 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 603 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.010   0.001   PHE A 411 
 TRP   0.009   0.001   TRP A 492 
 HIS   0.002   0.000   HIS B 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8836)
  covalent geometry    : angle       0.55118 (12036)
  hydrogen bonds       : bond        0.03549 (  518)
  hydrogen bonds       : angle       4.02214 ( 1518)
  link_BETA1-4         : bond        0.00290 (    2)
  link_BETA1-4         : angle       0.73675 (    6)
  link_NAG-ASN         : bond        0.00071 (    2)
  link_NAG-ASN         : angle       1.16446 (    6)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  554 ASN cc_start: 0.8363 (t0) cc_final: 0.7907 (t0)
REVERT: A  603 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8245 (mtm-85)
REVERT: B  554 ASN cc_start: 0.8360 (t0) cc_final: 0.7905 (t0)
REVERT: B  603 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8149 (mtm-85)
  outliers start: 15
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0814
  time to fit residues: 8.4823
Evaluate side-chains
  67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  431 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain B residue  780 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  873 LEU
Chi-restraints excluded: chain B residue  889 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0670
   chunk 89 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 88 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.3918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.072920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.062168 restraints weight = 25140.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 2.93
r_work: 0.2869 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8840  Z= 0.107
  Angle     :  0.549   9.091  12048  Z= 0.258
  Chirality :  0.039   0.306   1436
  Planarity :  0.005   0.048   1404
  Dihedral  :  8.354  86.900   1874
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.83 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.27), residues: 1024
  helix:  2.10 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.07 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 603 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.011   0.001   PHE A 411 
 TRP   0.009   0.001   TRP A 492 
 HIS   0.001   0.000   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8836)
  covalent geometry    : angle       0.54882 (12036)
  hydrogen bonds       : bond        0.03412 (  518)
  hydrogen bonds       : angle       3.97896 ( 1518)
  link_BETA1-4         : bond        0.00334 (    2)
  link_BETA1-4         : angle       0.76752 (    6)
  link_NAG-ASN         : bond        0.00082 (    2)
  link_NAG-ASN         : angle       1.20113 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1425.44 seconds
wall clock time: 25 minutes 17.17 seconds (1517.17 seconds total)