Starting phenix.real_space_refine
on Tue Mar  3 18:24:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xqn_67119/03_2026/9xqn_67119_neut.cif"
  }
  resolution = 3.91
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 14 atoms to isotropic.
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      18      5.16       5
     C    2555      2.51       5
     N     690      2.21       5
     O     782      1.98       5
     H    3653      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7698
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 4371
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 8, 'TRANS': 356}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 522
          Unresolved non-hydrogen angles: 665
          Unresolved non-hydrogen dihedrals: 453
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 6, 'HIS:plan': 3, 'ARG:plan': 8, 'TRP:plan': 2, 'GLU:plan': 7}
          Unresolved non-hydrogen planarities: 302
    Chain: "B"
      Number of atoms: 1569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 1569
          Classifications: {'peptide': 106}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1758
          Classifications: {'peptide': 121}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 1.55, per 1000 atoms: 0.20
  Number of scatterers: 7698
  At special positions: 0
  Unit cell: (68.62, 77.38, 139.43, 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      18     16.00
     O     782      8.00
     N     690      7.00
     C    2555      6.00
     H    3653      1.00
    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
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 204.0 milliseconds
  

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1114

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 4 sheets defined
      56.8% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 397 through 430
      removed outlier: 3.642A  pdb=" N   HIS A 401 " --> pdb=" O   GLN A 397 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU A 428 " --> pdb=" O   PHE A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 459
      removed outlier: 5.004A  pdb=" N   PHE A 455 " --> pdb=" O   PHE A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 469
    Processing helix  chain 'A' and resid 472 through 476
      removed outlier: 4.129A  pdb=" N   ILE A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 472 through 476'
    Processing helix  chain 'A' and resid 480 through 512
      removed outlier: 3.523A  pdb=" N   THR A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A 489 " --> pdb=" O   HIS A 485 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE A 492 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 544
      removed outlier: 4.044A  pdb=" N   LEU A 529 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 622
    Processing helix  chain 'A' and resid 625 through 646
    Processing helix  chain 'A' and resid 653 through 676
      removed outlier: 3.724A  pdb=" N   HIS A 659 " --> pdb=" O   LYS A 655 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A 660 " --> pdb=" O   ASP A 656 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE A 661 " --> pdb=" O   PHE A 657 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 674 " --> pdb=" O   ASP A 670 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA A 675 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 716
      removed outlier: 4.162A  pdb=" N   ALA A 696 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   TYR A 697 " --> pdb=" O   THR A 693 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 698 " --> pdb=" O   ARG A 694 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR A 708 " --> pdb=" O   ARG A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 741
      Proline residue:  A 732  - end of helix
      removed outlier: 3.548A  pdb=" N   VAL A 738 " --> pdb=" O   GLY A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 772
      removed outlier: 3.502A  pdb=" N   PHE A 762 " --> pdb=" O   PHE A 758 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER A 765 " --> pdb=" O   ILE A 761 " (cutoff:3.500A)
      Proline residue:  A 769  - end of helix
    Processing helix  chain 'A' and resid 775 through 786
      removed outlier: 4.184A  pdb=" N   TRP A 785 " --> pdb=" O   ARG A 781 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   CYS A 786 " --> pdb=" O   LYS A 782 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'C' and resid 107 through 111
      removed outlier: 3.662A  pdb=" N   TRP C 110 " --> pdb=" O   GLY C 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55
      removed outlier: 6.834A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   TYR B  50 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   VAL B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 8 through 9
      removed outlier: 3.870A  pdb=" N   VAL C   8 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   GLY C  19 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.471A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 124 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE C  37 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   TYR C  53 " --> pdb=" O   ILE C  37 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   TRP C  39 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    876 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 3640
        1.13 -     1.31: 675
        1.31 -     1.48: 1684
        1.48 -     1.65: 1735
        1.65 -     1.83: 23
  Bond restraints: 7757
  Sorted by residual:
  bond pdb=" N   ALA C 113 "
       pdb=" H   ALA C 113 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   LEU A 702 "
       pdb=" H   LEU A 702 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   PHE A 424 "
       pdb=" H   PHE A 424 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   GLN C  42 "
       pdb=" H   GLN C  42 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CD1 TRP C 110 "
       pdb=" HD1 TRP C 110 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  ... (remaining 7752 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 12178
        2.34 -     4.67: 788
        4.67 -     7.01: 874
        7.01 -     9.35: 45
        9.35 -    11.69: 2
  Bond angle restraints: 13887
  Sorted by residual:
  angle pdb=" CA  LEU A 750 "
        pdb=" C   LEU A 750 "
        pdb=" N   TYR A 751 "
      ideal   model   delta    sigma   weight residual
     118.14  124.60   -6.46 1.31e+00 5.83e-01 2.43e+01
  angle pdb=" N   THR A 407 "
        pdb=" CA  THR A 407 "
        pdb=" C   THR A 407 "
      ideal   model   delta    sigma   weight residual
     111.36  106.09    5.27 1.09e+00 8.42e-01 2.34e+01
  angle pdb=" N   VAL B  30 "
        pdb=" CA  VAL B  30 "
        pdb=" C   VAL B  30 "
      ideal   model   delta    sigma   weight residual
     111.88  107.23    4.65 1.06e+00 8.90e-01 1.92e+01
  angle pdb=" N   LEU A 411 "
        pdb=" CA  LEU A 411 "
        pdb=" C   LEU A 411 "
      ideal   model   delta    sigma   weight residual
     111.07  106.47    4.60 1.07e+00 8.73e-01 1.85e+01
  angle pdb=" N   ILE A 492 "
        pdb=" CA  ILE A 492 "
        pdb=" C   ILE A 492 "
      ideal   model   delta    sigma   weight residual
     110.42  114.22   -3.80 9.60e-01 1.09e+00 1.57e+01
  ... (remaining 13882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3440
       17.96 -    35.93: 186
       35.93 -    53.89: 68
       53.89 -    71.85: 66
       71.85 -    89.81: 11
  Dihedral angle restraints: 3771
    sinusoidal: 1845
      harmonic: 1926
  Sorted by residual:
  dihedral pdb=" CA  ILE A 456 "
           pdb=" C   ILE A 456 "
           pdb=" N   CYS A 457 "
           pdb=" CA  CYS A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.43   22.57     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  LYS A 545 "
           pdb=" C   LYS A 545 "
           pdb=" N   THR A 546 "
           pdb=" CA  THR A 546 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.50   22.50     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  SER A 765 "
           pdb=" C   SER A 765 "
           pdb=" N   GLY A 766 "
           pdb=" CA  GLY A 766 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 3768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 567
       0.067 -    0.133: 109
       0.133 -    0.200: 18
       0.200 -    0.267: 4
       0.267 -    0.333: 2
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" CA  PHE A 753 "
            pdb=" N   PHE A 753 "
            pdb=" C   PHE A 753 "
            pdb=" CB  PHE A 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  SER A 765 "
            pdb=" N   SER A 765 "
            pdb=" C   SER A 765 "
            pdb=" CB  SER A 765 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  LEU A 405 "
            pdb=" N   LEU A 405 "
            pdb=" C   LEU A 405 "
            pdb=" CB  LEU A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 697 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 574 "    0.075 2.00e-02 2.50e+03   2.95e-02 2.60e+01
        pdb=" CG  PHE A 574 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 574 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 574 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 574 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 574 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 574 "    0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 574 "   -0.012 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 574 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 574 "    0.013 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 574 "    0.010 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 574 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 770 "   -0.044 2.00e-02 2.50e+03   2.63e-02 2.08e+01
        pdb=" CG  PHE A 770 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 770 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 770 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 770 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 770 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 770 "   -0.013 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 770 "    0.050 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 770 "    0.013 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 770 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 770 "    0.034 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 770 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 545 "    0.024 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" N   THR A 546 "   -0.075 2.00e-02 2.50e+03
        pdb=" CA  THR A 546 "    0.022 2.00e-02 2.50e+03
        pdb=" H   THR A 546 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 443
        2.15 -     2.76: 12811
        2.76 -     3.38: 20783
        3.38 -     3.99: 26646
        3.99 -     4.60: 38938
  Nonbonded interactions: 99621
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 662 "
            pdb=" HE1 TRP C 105 "
     model   vdw
     1.540 2.450
  nonbonded pdb=" HG  CYS B  24 "
            pdb=" HB2 PHE B  72 "
     model   vdw
     1.651 2.440
  nonbonded pdb=" HE  ARG A 637 "
            pdb=" OD1 ASP A 669 "
     model   vdw
     1.658 2.450
  nonbonded pdb="HG21 VAL B  20 "
            pdb="HD12 LEU B  79 "
     model   vdw
     1.667 2.440
  nonbonded pdb=" O   HIS A 401 "
            pdb=" HG1 THR A 404 "
     model   vdw
     1.671 2.450
  ... (remaining 99616 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.05 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5727
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      :  0.007   0.036   4104  Z= 0.448
  Angle     :  1.167   6.638   5606  Z= 0.799
  Chirality :  0.058   0.333    700
  Planarity :  0.007   0.040    708
  Dihedral  :  8.654  63.027   1298
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.21 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.35), residues: 566
  helix:  0.63 (0.29), residues: 301
  sheet:  0.67 (0.54), residues: 104
  loop : -0.77 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 506 
 TYR   0.031   0.001   TYR A 772 
 PHE   0.050   0.004   PHE A 574 
 TRP   0.024   0.002   TRP A 785 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 ( 4104)
  covalent geometry    : angle       1.16723 ( 5606)
  hydrogen bonds       : bond        0.18350 (  305)
  hydrogen bonds       : angle       7.16284 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 CYS cc_start: 0.4912 (m) cc_final: 0.4698 (p)
REVERT: A  694 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.4393 (tmt170)
REVERT: B   48 LEU cc_start: 0.7810 (mt) cc_final: 0.7466 (mt)
REVERT: B   54 SER cc_start: 0.7720 (m) cc_final: 0.7121 (t)
REVERT: B   78 SER cc_start: 0.7627 (p) cc_final: 0.7376 (p)
REVERT: C    5 VAL cc_start: 0.7776 (t) cc_final: 0.7546 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1450
  time to fit residues: 15.1122
Evaluate side-chains
  77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  694 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
B 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.195341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.180118 restraints weight = 16968.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.184124 restraints weight = 8934.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.186499 restraints weight = 5395.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.187399 restraints weight = 3560.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.188667 restraints weight = 2887.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4290 r_free = 0.4290    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4282 r_free = 0.4282    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.4282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5816
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4104  Z= 0.184
  Angle     :  0.544   4.634   5606  Z= 0.298
  Chirality :  0.037   0.134    700
  Planarity :  0.004   0.037    708
  Dihedral  :  4.845  55.311    612
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.49 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.35), residues: 566
  helix:  1.48 (0.28), residues: 305
  sheet:  0.64 (0.54), residues: 97
  loop : -1.05 (0.47), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  25 
 TYR   0.022   0.002   TYR B  56 
 PHE   0.011   0.002   PHE C  35 
 TRP   0.010   0.002   TRP C  39 
 HIS   0.003   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4104)
  covalent geometry    : angle       0.54425 ( 5606)
  hydrogen bonds       : bond        0.04872 (  305)
  hydrogen bonds       : angle       4.79259 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  616 ASN cc_start: 0.5865 (t0) cc_final: 0.5271 (t0)
REVERT: A  694 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.4213 (tmt170)
REVERT: B   54 SER cc_start: 0.8019 (m) cc_final: 0.7705 (t)
REVERT: B   78 SER cc_start: 0.7693 (p) cc_final: 0.7476 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1314
  time to fit residues: 13.0982
Evaluate side-chains
  72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  694 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 32 optimal weight:    0.2980
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 644 GLN
** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.194159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.178523 restraints weight = 17142.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.182399 restraints weight = 9169.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.184798 restraints weight = 5574.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.186329 restraints weight = 3799.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.186958 restraints weight = 2784.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4268 r_free = 0.4268    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4266 r_free = 0.4266    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.4266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5871
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4104  Z= 0.160
  Angle     :  0.512   4.714   5606  Z= 0.277
  Chirality :  0.037   0.135    700
  Planarity :  0.004   0.048    708
  Dihedral  :  4.873  58.157    612
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.51 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.35), residues: 566
  helix:  1.64 (0.29), residues: 304
  sheet:  0.58 (0.53), residues: 96
  loop : -1.29 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 658 
 TYR   0.021   0.002   TYR B  56 
 PHE   0.012   0.002   PHE A 574 
 TRP   0.010   0.002   TRP C 110 
 HIS   0.003   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4104)
  covalent geometry    : angle       0.51151 ( 5606)
  hydrogen bonds       : bond        0.04380 (  305)
  hydrogen bonds       : angle       4.48487 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  694 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.3869 (tmt-80)
REVERT: B   54 SER cc_start: 0.8339 (m) cc_final: 0.8053 (t)
REVERT: B   78 SER cc_start: 0.7726 (p) cc_final: 0.7520 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1387
  time to fit residues: 13.1502
Evaluate side-chains
  76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  694 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 616 ASN ** 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 = 0.4294 r_free = 0.4294 target = 0.187966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.172556 restraints weight = 17026.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.176538 restraints weight = 9012.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.178952 restraints weight = 5441.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.180403 restraints weight = 3623.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.181502 restraints weight = 2696.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4200 r_free = 0.4200    target_work(ls_wunit_k1) = 0.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4200 r_free = 0.4200    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
r_final: 0.4200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5941
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4104  Z= 0.196
  Angle     :  0.549   4.963   5606  Z= 0.298
  Chirality :  0.038   0.141    700
  Planarity :  0.004   0.040    708
  Dihedral  :  5.111  56.546    612
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.86 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.35), residues: 566
  helix:  1.39 (0.29), residues: 305
  sheet:  0.57 (0.54), residues: 93
  loop : -1.62 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 658 
 TYR   0.029   0.003   TYR B  56 
 PHE   0.015   0.002   PHE C  35 
 TRP   0.014   0.002   TRP C 110 
 HIS   0.005   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4104)
  covalent geometry    : angle       0.54881 ( 5606)
  hydrogen bonds       : bond        0.04416 (  305)
  hydrogen bonds       : angle       4.58374 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7031 (tp) cc_final: 0.6704 (tp)
REVERT: A  694 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.4458 (tmt170)
REVERT: B   54 SER cc_start: 0.8472 (m) cc_final: 0.8238 (t)
REVERT: B   79 LEU cc_start: 0.8262 (mt) cc_final: 0.8045 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 76
  average time/residue: 0.1349
  time to fit residues: 12.9959
Evaluate side-chains
  76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain C residue   38 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 ASN ** 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 = 0.4276 r_free = 0.4276 target = 0.185940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.170669 restraints weight = 16842.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.174533 restraints weight = 9037.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.176803 restraints weight = 5494.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.178360 restraints weight = 3738.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.179216 restraints weight = 2730.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4217 r_free = 0.4217    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4218 r_free = 0.4218    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
r_final: 0.4218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5941
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4104  Z= 0.175
  Angle     :  0.510   5.151   5606  Z= 0.276
  Chirality :  0.037   0.137    700
  Planarity :  0.004   0.040    708
  Dihedral  :  5.024  56.877    612
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.33 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.35), residues: 566
  helix:  1.54 (0.29), residues: 305
  sheet:  0.42 (0.54), residues: 94
  loop : -1.69 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 658 
 TYR   0.023   0.002   TYR B  56 
 PHE   0.010   0.001   PHE A 574 
 TRP   0.010   0.002   TRP C 110 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4104)
  covalent geometry    : angle       0.51011 ( 5606)
  hydrogen bonds       : bond        0.04150 (  305)
  hydrogen bonds       : angle       4.48500 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7069 (tp) cc_final: 0.6730 (tp)
REVERT: A  694 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.4165 (tmt-80)
REVERT: B   54 SER cc_start: 0.8333 (m) cc_final: 0.8073 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1452
  time to fit residues: 12.8235
Evaluate side-chains
  70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 768 ASN ** 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 = 0.4302 r_free = 0.4302 target = 0.188551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.173154 restraints weight = 16739.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.176897 restraints weight = 8798.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.179393 restraints weight = 5302.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.180553 restraints weight = 3562.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.181678 restraints weight = 2737.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4218 r_free = 0.4218    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4218 r_free = 0.4218    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
r_final: 0.4218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5933
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4104  Z= 0.151
  Angle     :  0.480   4.718   5606  Z= 0.260
  Chirality :  0.036   0.136    700
  Planarity :  0.004   0.038    708
  Dihedral  :  4.910  58.053    612
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.05 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.36), residues: 566
  helix:  1.77 (0.29), residues: 306
  sheet:  0.47 (0.54), residues: 94
  loop : -1.84 (0.46), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 658 
 TYR   0.020   0.002   TYR B  56 
 PHE   0.009   0.001   PHE A 661 
 TRP   0.009   0.002   TRP B  36 
 HIS   0.005   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4104)
  covalent geometry    : angle       0.47977 ( 5606)
  hydrogen bonds       : bond        0.03837 (  305)
  hydrogen bonds       : angle       4.28083 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7078 (tp) cc_final: 0.6758 (tp)
REVERT: A  673 LYS cc_start: 0.7070 (ttmm) cc_final: 0.6827 (ttmt)
REVERT: A  694 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.4181 (tmt-80)
REVERT: B   54 SER cc_start: 0.8284 (m) cc_final: 0.7994 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 74
  average time/residue: 0.1321
  time to fit residues: 12.3681
Evaluate side-chains
  73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain C residue  122 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 616 ASN
** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.187452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.172114 restraints weight = 16677.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.175973 restraints weight = 8794.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.178361 restraints weight = 5251.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.179898 restraints weight = 3524.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.180368 restraints weight = 2544.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4180 r_free = 0.4180    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4179 r_free = 0.4179    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.4179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5969
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4104  Z= 0.179
  Angle     :  0.510   5.104   5606  Z= 0.276
  Chirality :  0.037   0.138    700
  Planarity :  0.004   0.039    708
  Dihedral  :  5.061  58.284    612
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.33 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.36), residues: 566
  helix:  1.66 (0.29), residues: 307
  sheet:  0.37 (0.55), residues: 94
  loop : -1.95 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 658 
 TYR   0.025   0.002   TYR B  56 
 PHE   0.012   0.002   PHE A 661 
 TRP   0.010   0.002   TRP B  36 
 HIS   0.005   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4104)
  covalent geometry    : angle       0.50990 ( 5606)
  hydrogen bonds       : bond        0.04074 (  305)
  hydrogen bonds       : angle       4.44795 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7062 (tp) cc_final: 0.6744 (tp)
REVERT: A  644 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7740 (tt0)
REVERT: A  673 LYS cc_start: 0.6996 (ttmm) cc_final: 0.6788 (ttmt)
REVERT: A  694 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.4093 (tmt-80)
REVERT: B   54 SER cc_start: 0.8536 (m) cc_final: 0.8263 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1338
  time to fit residues: 12.3193
Evaluate side-chains
  74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  644 GLN
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue  122 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0970
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.189849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.174090 restraints weight = 17025.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.177988 restraints weight = 9074.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.180391 restraints weight = 5472.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.181991 restraints weight = 3672.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.182604 restraints weight = 2650.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4228 r_free = 0.4228    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4229 r_free = 0.4229    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.4229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5956
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4104  Z= 0.149
  Angle     :  0.478   4.777   5606  Z= 0.258
  Chirality :  0.036   0.135    700
  Planarity :  0.004   0.037    708
  Dihedral  :  4.927  58.686    612
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.60 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.36), residues: 566
  helix:  1.80 (0.29), residues: 308
  sheet:  0.76 (0.56), residues: 89
  loop : -2.04 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 658 
 TYR   0.018   0.002   TYR B  56 
 PHE   0.009   0.001   PHE A 661 
 TRP   0.008   0.002   TRP C 117 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4104)
  covalent geometry    : angle       0.47847 ( 5606)
  hydrogen bonds       : bond        0.03748 (  305)
  hydrogen bonds       : angle       4.26327 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7067 (tp) cc_final: 0.6755 (tp)
REVERT: A  694 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.4177 (tmt-80)
REVERT: B   54 SER cc_start: 0.8406 (m) cc_final: 0.8136 (t)
  outliers start: 7
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1320
  time to fit residues: 12.3885
Evaluate side-chains
  76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue  102 TRP
Chi-restraints excluded: chain C residue  122 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** 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 = 0.4260 r_free = 0.4260 target = 0.183469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.168611 restraints weight = 16883.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.172187 restraints weight = 9169.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.173722 restraints weight = 5635.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.175430 restraints weight = 4185.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.176692 restraints weight = 3069.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.4199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6006
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4104  Z= 0.228
  Angle     :  0.550   5.235   5606  Z= 0.304
  Chirality :  0.038   0.141    700
  Planarity :  0.004   0.039    708
  Dihedral  :  5.349  57.726    612
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.23 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.35), residues: 566
  helix:  1.31 (0.29), residues: 305
  sheet:  0.42 (0.56), residues: 89
  loop : -2.28 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 637 
 TYR   0.031   0.003   TYR B  56 
 PHE   0.014   0.002   PHE A 661 
 TRP   0.013   0.003   TRP C 110 
 HIS   0.005   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 4104)
  covalent geometry    : angle       0.55011 ( 5606)
  hydrogen bonds       : bond        0.04482 (  305)
  hydrogen bonds       : angle       4.75105 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7048 (tp) cc_final: 0.6733 (tp)
REVERT: A  630 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7298 (ttpp)
REVERT: A  644 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7891 (tt0)
REVERT: A  694 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.4401 (tmt170)
REVERT: B   54 SER cc_start: 0.8497 (m) cc_final: 0.8277 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1246
  time to fit residues: 11.3662
Evaluate side-chains
  74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  644 GLN
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   41 ARG
Chi-restraints excluded: chain C residue  102 TRP
Chi-restraints excluded: chain C residue  122 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
C  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.188671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.173258 restraints weight = 16761.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.177030 restraints weight = 8922.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.179189 restraints weight = 5430.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.180866 restraints weight = 3712.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.181690 restraints weight = 2695.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.4207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5965
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4104  Z= 0.147
  Angle     :  0.486   5.048   5606  Z= 0.263
  Chirality :  0.036   0.137    700
  Planarity :  0.004   0.038    708
  Dihedral  :  5.038  58.335    612
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.78 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.36), residues: 566
  helix:  1.67 (0.29), residues: 308
  sheet:  0.44 (0.56), residues: 94
  loop : -2.18 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 637 
 TYR   0.018   0.002   TYR B  56 
 PHE   0.010   0.001   PHE A 661 
 TRP   0.009   0.002   TRP B  36 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4104)
  covalent geometry    : angle       0.48592 ( 5606)
  hydrogen bonds       : bond        0.03798 (  305)
  hydrogen bonds       : angle       4.39589 (  876)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  399 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue THR  402 is missing expected H atoms. Skipping.
Residue VAL  406 is missing expected H atoms. Skipping.
Residue THR  409 is missing expected H atoms. Skipping.
Residue LEU  411 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue ILE  415 is missing expected H atoms. Skipping.
Residue SER  420 is missing expected H atoms. Skipping.
Residue TYR  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue LEU  428 is missing expected H atoms. Skipping.
Residue SER  429 is missing expected H atoms. Skipping.
Residue MET  445 is missing expected H atoms. Skipping.
Residue ILE  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue THR  465 is missing expected H atoms. Skipping.
Residue VAL  467 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue ILE  476 is missing expected H atoms. Skipping.
Residue THR  487 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  494 is missing expected H atoms. Skipping.
Residue SER  495 is missing expected H atoms. Skipping.
Residue LYS  497 is missing expected H atoms. Skipping.
Residue LEU  504 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue LEU  511 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  526 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  530 is missing expected H atoms. Skipping.
Residue LEU  538 is missing expected H atoms. Skipping.
Residue THR  540 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue LEU  551 is missing expected H atoms. Skipping.
Residue LEU  553 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue SER  557 is missing expected H atoms. Skipping.
Residue LEU  558 is missing expected H atoms. Skipping.
Residue LYS  562 is missing expected H atoms. Skipping.
Residue LYS  564 is missing expected H atoms. Skipping.
Residue LEU  569 is missing expected H atoms. Skipping.
Residue TYR  570 is missing expected H atoms. Skipping.
Residue VAL  572 is missing expected H atoms. Skipping.
Residue VAL  580 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue TYR  585 is missing expected H atoms. Skipping.
Residue MET  587 is missing expected H atoms. Skipping.
Residue THR  591 is missing expected H atoms. Skipping.
Residue LYS  594 is missing expected H atoms. Skipping.
Residue LYS  618 is missing expected H atoms. Skipping.
Residue LEU  664 is missing expected H atoms. Skipping.
Residue LYS  681 is missing expected H atoms. Skipping.
Residue LYS  691 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue LYS  711 is missing expected H atoms. Skipping.
Residue VAL  720 is missing expected H atoms. Skipping.
Residue ILE  721 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue LEU  731 is missing expected H atoms. Skipping.
Residue TYR  751 is missing expected H atoms. Skipping.
Residue LEU  760 is missing expected H atoms. Skipping.
Residue LYS  782 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue SER    1 is missing expected H atoms. Skipping.
Residue LYS   68 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  567 LEU cc_start: 0.7067 (tp) cc_final: 0.6760 (tp)
REVERT: A  630 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7307 (ttpp)
REVERT: A  644 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7783 (tt0)
REVERT: A  694 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.4204 (tmt-80)
REVERT: B   54 SER cc_start: 0.8480 (m) cc_final: 0.8261 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1411
  time to fit residues: 13.2495
Evaluate side-chains
  74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  644 GLN
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  694 ARG
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain C residue   38 HIS
Chi-restraints excluded: chain C residue   41 ARG
Chi-restraints excluded: chain C residue  102 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.181251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.167001 restraints weight = 16582.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.170641 restraints weight = 8881.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.172715 restraints weight = 5397.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.174011 restraints weight = 3661.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.175136 restraints weight = 2778.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4184 r_free = 0.4184    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4185 r_free = 0.4185    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.4185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
moved from start:          0.5167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4104  Z= 0.234
  Angle     :  0.548   5.227   5606  Z= 0.303
  Chirality :  0.038   0.142    700
  Planarity :  0.004   0.039    708
  Dihedral  :  5.366  57.740    612
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.78 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.35), residues: 566
  helix:  1.24 (0.29), residues: 305
  sheet:  0.15 (0.54), residues: 94
  loop : -2.41 (0.45), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 637 
 TYR   0.031   0.003   TYR B  56 
 PHE   0.014   0.002   PHE A 661 
 TRP   0.014   0.003   TRP C 110 
 HIS   0.004   0.002   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 4104)
  covalent geometry    : angle       0.54829 ( 5606)
  hydrogen bonds       : bond        0.04430 (  305)
  hydrogen bonds       : angle       4.78013 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1689.40 seconds
wall clock time: 29 minutes 22.56 seconds (1762.56 seconds total)