Starting phenix.real_space_refine
on Thu Jul  2 08:12:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rvy_54292/07_2026/9rvy_54292.map"
  }
  resolution = 3.0
  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=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     S      33      5.16       5
     C    4487      2.51       5
     N    1311      2.21       5
     O    1710      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7629
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 426
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 433
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 3700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3700
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "C"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1220
          Classifications: {'peptide': 152}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 147}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
    Chain: "F"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
  Time building chain proxies: 1.90, per 1000 atoms: 0.25
  Number of scatterers: 7629
  At special positions: 0
  Unit cell: (78.366, 97.428, 152.496, 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      33     16.00
     P      88     15.00
     O    1710      8.00
     N    1311      7.00
     C    4487      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 353.1 milliseconds
  

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      70.0% alpha, 6.1% beta
      34 base pairs and 54 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.658A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 3.786A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 43 through 51
    Processing helix  chain 'D' and resid 53 through 62
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.846A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 129
    Processing helix  chain 'D' and resid 130 through 138
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'D' and resid 521 through 530
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.845A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 617 through 628
      removed outlier: 4.795A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
      removed outlier: 3.613A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 676 through 680
    Processing helix  chain 'D' and resid 681 through 688
      removed outlier: 3.983A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.166A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 4.011A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 802
      removed outlier: 4.245A  pdb=" N   GLY D 802 " --> pdb=" O   GLU D 798 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 36 through 39
    Processing helix  chain 'C' and resid 42 through 50
      removed outlier: 3.995A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 4.091A  pdb=" N   TYR C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 110
      removed outlier: 3.719A  pdb=" N   GLN C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
      removed outlier: 4.015A  pdb=" N   LEU C 122 " --> pdb=" O   PRO C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 138
    Processing helix  chain 'C' and resid 140 through 151
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533
      removed outlier: 3.587A  pdb=" N   LEU D 587 " --> pdb=" O   THR D 531 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158

    372 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      54 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.12 -     1.25: 1088
        1.25 -     1.39: 1983
        1.39 -     1.53: 4499
        1.53 -     1.67: 304
        1.67 -     1.81: 54
  Bond restraints: 7928
  Sorted by residual:
  bond pdb=" C   ASP C  32 "
       pdb=" O   ASP C  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.115  0.121 1.26e-02 6.30e+03 9.20e+01
  bond pdb=" C   SER C  34 "
       pdb=" O   SER C  34 "
    ideal  model  delta    sigma   weight residual
    1.236  1.115  0.121 1.32e-02 5.74e+03 8.35e+01
  bond pdb=" C   MET C   8 "
       pdb=" O   MET C   8 "
    ideal  model  delta    sigma   weight residual
    1.237  1.139  0.097 1.19e-02 7.06e+03 6.71e+01
  bond pdb=" CA  GLU D  45 "
       pdb=" C   GLU D  45 "
    ideal  model  delta    sigma   weight residual
    1.524  1.426  0.098 1.26e-02 6.30e+03 6.02e+01
  bond pdb=" CA  SER C  34 "
       pdb=" C   SER C  34 "
    ideal  model  delta    sigma   weight residual
    1.522  1.417  0.105 1.39e-02 5.18e+03 5.70e+01
  ... (remaining 7923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 10916
        2.52 -     5.05: 155
        5.05 -     7.57: 12
        7.57 -    10.09: 1
       10.09 -    12.62: 2
  Bond angle restraints: 11086
  Sorted by residual:
  angle pdb=" O3'   C E  33 "
        pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     113.70  126.32  -12.62 1.50e+00 4.44e-01 7.08e+01
  angle pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
        pdb=" O2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     110.70  120.63   -9.93 1.50e+00 4.44e-01 4.38e+01
  angle pdb=" N6    A F  31 "
        pdb=" C6    A F  31 "
        pdb=" N1    A F  31 "
      ideal   model   delta    sigma   weight residual
     118.60  114.88    3.72 6.00e-01 2.78e+00 3.85e+01
  angle pdb=" N6    A F  30 "
        pdb=" C6    A F  30 "
        pdb=" N1    A F  30 "
      ideal   model   delta    sigma   weight residual
     118.60  115.08    3.52 6.00e-01 2.78e+00 3.44e+01
  angle pdb=" N6    A F  37 "
        pdb=" C6    A F  37 "
        pdb=" N1    A F  37 "
      ideal   model   delta    sigma   weight residual
     118.60  115.12    3.48 6.00e-01 2.78e+00 3.37e+01
  ... (remaining 11081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.79: 4619
       35.79 -    71.59: 240
       71.59 -   107.38: 21
      107.38 -   143.18: 0
      143.18 -   178.97: 2
  Dihedral angle restraints: 4882
    sinusoidal: 2766
      harmonic: 2116
  Sorted by residual:
  dihedral pdb=" C4'   C F  33 "
           pdb=" C3'   C F  33 "
           pdb=" O3'   C F  33 "
           pdb=" P     U F  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.97 -178.97     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C5'   C E  33 "
           pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" O3'   C E  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00   55.93   26.07     1      8.00e+00 1.56e-02 1.53e+01
  dihedral pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" O3'   C E  33 "
           pdb=" P     U E  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.43  158.57     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 4879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1304
       0.118 -    0.236: 12
       0.236 -    0.354: 4
       0.354 -    0.472: 2
       0.472 -    0.590: 1
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" C3'   C E  33 "
            pdb=" C4'   C E  33 "
            pdb=" O3'   C E  33 "
            pdb=" C2'   C E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.89   -0.59 2.00e-01 2.50e+01 8.70e+00
  chirality pdb=" CA  SER C  34 "
            pdb=" N   SER C  34 "
            pdb=" C   SER C  34 "
            pdb=" CB  SER C  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" CA  ARG D 120 "
            pdb=" N   ARG D 120 "
            pdb=" C   ARG D 120 "
            pdb=" CB  ARG D 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  ... (remaining 1320 not shown)

  Planarity restraints: 1106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  17 "    0.064 2.00e-02 2.50e+03   2.58e-02 1.84e+01
        pdb=" N9    A F  17 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8    A F  17 "   -0.020 2.00e-02 2.50e+03
        pdb=" N7    A F  17 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    A F  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A F  17 "    0.006 2.00e-02 2.50e+03
        pdb=" N6    A F  17 "    0.033 2.00e-02 2.50e+03
        pdb=" N1    A F  17 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A F  17 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3    A F  17 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4    A F  17 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F  11 "   -0.057 2.00e-02 2.50e+03   2.65e-02 1.58e+01
        pdb=" N1    U F  11 "    0.043 2.00e-02 2.50e+03
        pdb=" C2    U F  11 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    U F  11 "    0.016 2.00e-02 2.50e+03
        pdb=" N3    U F  11 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    U F  11 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U F  11 "   -0.022 2.00e-02 2.50e+03
        pdb=" C5    U F  11 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    U F  11 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  35 "    0.057 2.00e-02 2.50e+03   2.33e-02 1.49e+01
        pdb=" N9    A F  35 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    A F  35 "   -0.012 2.00e-02 2.50e+03
        pdb=" N7    A F  35 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    A F  35 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6    A F  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A F  35 "    0.033 2.00e-02 2.50e+03
        pdb=" N1    A F  35 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    A F  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    A F  35 "   -0.015 2.00e-02 2.50e+03
        pdb=" C4    A F  35 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1103 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 170
        2.66 -     3.22: 7320
        3.22 -     3.78: 12620
        3.78 -     4.34: 16937
        4.34 -     4.90: 26125
  Nonbonded interactions: 63172
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 160 "
            pdb=" OD1 ASP C 160 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O2'   C E  36 "
            pdb=" OP1   A E  38 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   ASP D 589 "
            pdb=" OG  SER D 592 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   PHE C  42 "
            pdb=" OG1 THR C  43 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASP D 160 "
            pdb=" OD1 ASP D 160 "
     model   vdw
     2.321 3.040
  ... (remaining 63167 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 695 through 740 or (resid 741 through 742 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 743 through 747))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.900
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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   0.128   7928  Z= 0.526
  Angle     :  0.756  12.618  11086  Z= 0.663
  Chirality :  0.048   0.590   1323
  Planarity :  0.005   0.095   1106
  Dihedral  : 19.035 178.970   3508
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 24.76 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.32), residues: 704
  helix:  1.67 (0.25), residues: 460
  sheet: -0.74 (0.92), residues: 28
  loop : -0.93 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D 634 
 TYR   0.012   0.001   TYR D   6 
 PHE   0.013   0.001   PHE C 104 
 TRP   0.002   0.001   TRP D 522 
 HIS   0.012   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00702 /  0.53 ( 7928)
  covalent geometry    : angle       0.75580 /  0.66 (11086)
  hydrogen bonds       : bond        0.11488 /  7.85 (  444)
  hydrogen bonds       : angle       5.49621 /  3.73 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: D  634 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7542 (ttm110)
REVERT: D  660 TYR cc_start: 0.8227 (m-80) cc_final: 0.7978 (m-80)
  outliers start: 2
  outliers final: 3
  residues processed: 108
  average time/residue: 0.6421
  time to fit residues: 72.8201
Evaluate side-chains
  96 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  718 PHE
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.1682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 708 GLN
D 714 HIS
C 106 ASN
C 140 HIS
C 151 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.185026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.137661 restraints weight = 10539.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.41
r_work: 0.3262 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7928  Z= 0.158
  Angle     :  0.553   7.580  11086  Z= 0.311
  Chirality :  0.039   0.226   1323
  Planarity :  0.004   0.050   1106
  Dihedral  : 16.422 179.823   2055
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.83 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.32), residues: 704
  helix:  1.92 (0.24), residues: 460
  sheet: -0.97 (0.97), residues: 25
  loop : -0.63 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 730 
 TYR   0.012   0.001   TYR C   6 
 PHE   0.021   0.002   PHE C 104 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 714 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.16 ( 7928)
  covalent geometry    : angle       0.55346 /  0.31 (11086)
  hydrogen bonds       : bond        0.05072 /  3.37 (  444)
  hydrogen bonds       : angle       4.49485 /  3.08 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.249 
Fit side-chains
REVERT: D  621 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6484 (p0)
REVERT: D  634 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7497 (ttm110)
REVERT: D  743 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7835 (ttp)
REVERT: D  798 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: D  801 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7577 (mptt)
REVERT: C   29 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8384 (m)
REVERT: C   99 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7240 (mt-10)
REVERT: C  110 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7665 (pp30)
REVERT: C  149 MET cc_start: 0.6574 (tmm) cc_final: 0.6098 (mmt)
  outliers start: 20
  outliers final: 8
  residues processed: 108
  average time/residue: 0.5939
  time to fit residues: 67.5819
Evaluate side-chains
  105 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  718 PHE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  801 LYS
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   chunk 68 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 13 optimal weight:    0.5980
   chunk 78 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 706 ASN
A 708 GLN
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.186363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.139490 restraints weight = 10571.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.51
r_work: 0.3278 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7928  Z= 0.119
  Angle     :  0.489   7.287  11086  Z= 0.275
  Chirality :  0.036   0.183   1323
  Planarity :  0.004   0.035   1106
  Dihedral  : 16.407 177.661   2053
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.83 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.32), residues: 704
  helix:  2.05 (0.24), residues: 462
  sheet: -0.69 (0.91), residues: 28
  loop : -0.57 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 619 
 TYR   0.016   0.001   TYR D 660 
 PHE   0.027   0.002   PHE D 588 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 7928)
  covalent geometry    : angle       0.48904 /  0.27 (11086)
  hydrogen bonds       : bond        0.04494 /  2.99 (  444)
  hydrogen bonds       : angle       4.27684 /  2.93 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  621 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6298 (p0)
REVERT: D  634 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7485 (ttm110)
REVERT: D  743 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (ttp)
REVERT: D  798 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: D  801 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7592 (mptt)
REVERT: C    8 MET cc_start: 0.8878 (tpp) cc_final: 0.8666 (tpt)
REVERT: C   29 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8292 (m)
REVERT: C  110 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7624 (pp30)
REVERT: C  134 ARG cc_start: 0.8195 (ttp-170) cc_final: 0.7989 (ttp-170)
REVERT: C  149 MET cc_start: 0.6510 (tmm) cc_final: 0.6017 (mmt)
  outliers start: 22
  outliers final: 10
  residues processed: 108
  average time/residue: 0.5915
  time to fit residues: 66.9798
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  801 LYS
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.0770
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.6144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 708 GLN
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.184272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.137578 restraints weight = 10634.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.71
r_work: 0.3227 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7928  Z= 0.177
  Angle     :  0.519   7.762  11086  Z= 0.285
  Chirality :  0.038   0.167   1323
  Planarity :  0.004   0.038   1106
  Dihedral  : 16.376 174.572   2051
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.27 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.15 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.32), residues: 704
  helix:  2.01 (0.24), residues: 459
  sheet: -0.71 (0.92), residues: 28
  loop : -0.43 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 730 
 TYR   0.029   0.002   TYR D 393 
 PHE   0.016   0.002   PHE D 718 
 TRP   0.008   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 ( 7928)
  covalent geometry    : angle       0.51897 /  0.28 (11086)
  hydrogen bonds       : bond        0.04829 /  3.19 (  444)
  hydrogen bonds       : angle       4.32890 /  2.98 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: D  621 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6237 (p0)
REVERT: D  634 ARG cc_start: 0.8002 (mtp-110) cc_final: 0.7601 (ttm110)
REVERT: D  730 ARG cc_start: 0.7554 (mmt90) cc_final: 0.7196 (mmt90)
REVERT: D  743 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7882 (ttp)
REVERT: D  798 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: D  801 LYS cc_start: 0.7929 (mptm) cc_final: 0.7531 (mptt)
REVERT: C   29 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8341 (m)
REVERT: C  108 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4322 (tmm)
REVERT: C  110 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7592 (pp30)
REVERT: C  149 MET cc_start: 0.6651 (tmm) cc_final: 0.6148 (mmt)
  outliers start: 24
  outliers final: 14
  residues processed: 107
  average time/residue: 0.5246
  time to fit residues: 59.1571
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  718 PHE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 706 ASN
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.185683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.138038 restraints weight = 10526.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.86
r_work: 0.3234 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7928  Z= 0.137
  Angle     :  0.502   7.902  11086  Z= 0.277
  Chirality :  0.037   0.149   1323
  Planarity :  0.004   0.035   1106
  Dihedral  : 16.429 173.355   2051
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.12 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.28 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.32), residues: 704
  helix:  2.05 (0.24), residues: 459
  sheet: -0.84 (0.91), residues: 28
  loop : -0.34 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 799 
 TYR   0.018   0.001   TYR D 393 
 PHE   0.030   0.002   PHE D 718 
 TRP   0.011   0.002   TRP D 692 
 HIS   0.003   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 7928)
  covalent geometry    : angle       0.50219 /  0.28 (11086)
  hydrogen bonds       : bond        0.04473 /  2.97 (  444)
  hydrogen bonds       : angle       4.26071 /  2.94 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  745 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6209 (mp0)
REVERT: B  698 TYR cc_start: 0.7136 (t80) cc_final: 0.6915 (t80)
REVERT: D  621 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6205 (p0)
REVERT: D  633 LEU cc_start: 0.8653 (mt) cc_final: 0.8409 (mp)
REVERT: D  634 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7506 (ttm110)
REVERT: D  730 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7124 (mmt90)
REVERT: D  743 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7819 (ttp)
REVERT: D  798 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7871 (tm-30)
REVERT: D  801 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7434 (mptt)
REVERT: C   29 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8296 (m)
REVERT: C  108 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4243 (tmm)
REVERT: C  110 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7576 (pp30)
REVERT: C  141 ILE cc_start: 0.7786 (mp) cc_final: 0.7578 (tt)
REVERT: C  149 MET cc_start: 0.6601 (tmm) cc_final: 0.6049 (mmt)
  outliers start: 28
  outliers final: 10
  residues processed: 110
  average time/residue: 0.5143
  time to fit residues: 59.4854
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  533 ILE
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  698 THR
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  801 LYS
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.185624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.139055 restraints weight = 10626.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 3.03
r_work: 0.3216 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7928  Z= 0.134
  Angle     :  0.503   8.371  11086  Z= 0.274
  Chirality :  0.036   0.144   1323
  Planarity :  0.004   0.037   1106
  Dihedral  : 16.418 172.136   2051
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.12 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.60 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.32), residues: 704
  helix:  2.04 (0.24), residues: 459
  sheet: -0.81 (0.92), residues: 28
  loop : -0.32 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 788 
 TYR   0.011   0.001   TYR D 393 
 PHE   0.015   0.002   PHE D 586 
 TRP   0.011   0.001   TRP D 692 
 HIS   0.004   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 7928)
  covalent geometry    : angle       0.50319 /  0.27 (11086)
  hydrogen bonds       : bond        0.04408 /  2.91 (  444)
  hydrogen bonds       : angle       4.18539 /  2.88 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: D  621 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6216 (p0)
REVERT: D  633 LEU cc_start: 0.8671 (mt) cc_final: 0.8408 (mp)
REVERT: D  634 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7540 (ttm110)
REVERT: D  730 ARG cc_start: 0.7537 (mmt90) cc_final: 0.7154 (mmt90)
REVERT: D  743 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7832 (ttp)
REVERT: D  798 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: D  801 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7480 (mptt)
REVERT: C   29 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8315 (m)
REVERT: C  108 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4203 (tmm)
REVERT: C  110 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7636 (pp30)
REVERT: C  149 MET cc_start: 0.6613 (tmm) cc_final: 0.6049 (mmt)
  outliers start: 29
  outliers final: 14
  residues processed: 109
  average time/residue: 0.5450
  time to fit residues: 62.6763
Evaluate side-chains
  109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  533 ILE
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  698 THR
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  801 LYS
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 35 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.186846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139789 restraints weight = 10535.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.86
r_work: 0.3260 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7928  Z= 0.112
  Angle     :  0.488   8.603  11086  Z= 0.267
  Chirality :  0.035   0.126   1323
  Planarity :  0.003   0.040   1106
  Dihedral  : 16.427 171.004   2051
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.98 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 25.40 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.32), residues: 704
  helix:  2.17 (0.24), residues: 459
  sheet: -0.96 (0.89), residues: 28
  loop : -0.24 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.013   0.001   TYR D 660 
 PHE   0.016   0.002   PHE D 718 
 TRP   0.012   0.002   TRP D 692 
 HIS   0.004   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 7928)
  covalent geometry    : angle       0.48791 /  0.27 (11086)
  hydrogen bonds       : bond        0.04100 /  2.70 (  444)
  hydrogen bonds       : angle       4.08184 /  2.82 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   44 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8091 (mtmt)
REVERT: D  621 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6308 (p0)
REVERT: D  633 LEU cc_start: 0.8672 (mt) cc_final: 0.8449 (mp)
REVERT: D  634 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7505 (ttm110)
REVERT: D  668 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: D  743 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7815 (ttp)
REVERT: D  790 MET cc_start: 0.8375 (mtp) cc_final: 0.8159 (mtp)
REVERT: C   29 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8249 (m)
REVERT: C  108 MET cc_start: 0.5014 (OUTLIER) cc_final: 0.4270 (tmm)
REVERT: C  110 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7617 (pp30)
REVERT: C  149 MET cc_start: 0.6521 (tmm) cc_final: 0.5987 (mmt)
  outliers start: 28
  outliers final: 12
  residues processed: 112
  average time/residue: 0.5059
  time to fit residues: 59.7418
Evaluate side-chains
  109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  698 THR
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 77 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0370
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7062

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.186787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.139515 restraints weight = 10609.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.62
r_work: 0.3278 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7928  Z= 0.122
  Angle     :  0.511   8.832  11086  Z= 0.276
  Chirality :  0.036   0.161   1323
  Planarity :  0.004   0.076   1106
  Dihedral  : 16.398 169.539   2051
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.70 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.37 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.32), residues: 704
  helix:  2.16 (0.24), residues: 459
  sheet: -0.99 (0.91), residues: 26
  loop : -0.28 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG D  47 
 TYR   0.012   0.001   TYR D 660 
 PHE   0.018   0.002   PHE C 104 
 TRP   0.012   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 7928)
  covalent geometry    : angle       0.51136 /  0.28 (11086)
  hydrogen bonds       : bond        0.04134 /  2.72 (  444)
  hydrogen bonds       : angle       4.11773 /  2.83 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  745 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6217 (mp0)
REVERT: D   44 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8030 (mtmt)
REVERT: D  621 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6325 (p0)
REVERT: D  633 LEU cc_start: 0.8725 (mt) cc_final: 0.8511 (mp)
REVERT: D  634 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7606 (ttm110)
REVERT: D  668 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: D  730 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7308 (mmt90)
REVERT: D  743 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7822 (ttp)
REVERT: C   29 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (m)
REVERT: C  108 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4454 (tmm)
REVERT: C  110 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7617 (pp30)
REVERT: C  149 MET cc_start: 0.6539 (tmm) cc_final: 0.6017 (mmt)
  outliers start: 27
  outliers final: 12
  residues processed: 106
  average time/residue: 0.5103
  time to fit residues: 56.9414
Evaluate side-chains
  107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  745 GLU
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  698 THR
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   chunk 47 optimal weight:    0.0570
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.185892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138233 restraints weight = 10550.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.62
r_work: 0.3258 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7928  Z= 0.136
  Angle     :  0.505   9.120  11086  Z= 0.273
  Chirality :  0.036   0.189   1323
  Planarity :  0.004   0.070   1106
  Dihedral  : 16.394 167.917   2051
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.70 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 27.49 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.32), residues: 704
  helix:  2.10 (0.24), residues: 459
  sheet: -1.02 (0.90), residues: 26
  loop : -0.28 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  47 
 TYR   0.012   0.001   TYR D 660 
 PHE   0.029   0.002   PHE D 718 
 TRP   0.009   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 7928)
  covalent geometry    : angle       0.50499 /  0.27 (11086)
  hydrogen bonds       : bond        0.04229 /  2.79 (  444)
  hydrogen bonds       : angle       4.12619 /  2.85 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   44 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8090 (mtmt)
REVERT: D  621 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6324 (p0)
REVERT: D  634 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7571 (ttm110)
REVERT: D  730 ARG cc_start: 0.7768 (mmt90) cc_final: 0.7334 (mmt90)
REVERT: D  743 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7801 (ttp)
REVERT: C   29 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8280 (m)
REVERT: C  108 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4233 (tmm)
REVERT: C  110 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7590 (pp30)
REVERT: C  149 MET cc_start: 0.6574 (tmm) cc_final: 0.6034 (mmt)
  outliers start: 21
  outliers final: 12
  residues processed: 104
  average time/residue: 0.5638
  time to fit residues: 61.6508
Evaluate side-chains
  104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  698 THR
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  162 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 34 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 76 optimal weight:   20.0000
   chunk 11 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 728 GLN
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.186644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.139964 restraints weight = 10577.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.65
r_work: 0.3269 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7928  Z= 0.131
  Angle     :  0.526   9.167  11086  Z= 0.281
  Chirality :  0.036   0.220   1323
  Planarity :  0.004   0.068   1106
  Dihedral  : 16.401 167.111   2051
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.70 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 28.94 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.32), residues: 704
  helix:  2.12 (0.24), residues: 458
  sheet: -1.14 (0.88), residues: 26
  loop : -0.33 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  47 
 TYR   0.012   0.001   TYR D 660 
 PHE   0.018   0.002   PHE D 586 
 TRP   0.011   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 7928)
  covalent geometry    : angle       0.52637 /  0.28 (11086)
  hydrogen bonds       : bond        0.04095 /  2.70 (  444)
  hydrogen bonds       : angle       4.10653 /  2.84 ( 1207)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   44 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8069 (mtmt)
REVERT: D  634 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7478 (ttm110)
REVERT: D  730 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7305 (mmt90)
REVERT: D  743 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7810 (ttp)
REVERT: C   29 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8265 (m)
REVERT: C   46 MET cc_start: 0.8836 (mtp) cc_final: 0.8608 (ptp)
REVERT: C  108 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4296 (tmm)
REVERT: C  110 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7651 (pp30)
REVERT: C  149 MET cc_start: 0.6629 (tmm) cc_final: 0.6131 (mmt)
  outliers start: 16
  outliers final: 10
  residues processed: 99
  average time/residue: 0.5493
  time to fit residues: 57.1890
Evaluate side-chains
  103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  728 GLN
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0870
   chunk 49 optimal weight:    0.0470
   chunk 31 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 72 optimal weight:    6.9990
   overall best weight:    0.6058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.187106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.140537 restraints weight = 10567.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.57
r_work: 0.3283 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7928  Z= 0.119
  Angle     :  0.522   9.256  11086  Z= 0.278
  Chirality :  0.035   0.238   1323
  Planarity :  0.004   0.065   1106
  Dihedral  : 16.407 166.726   2051
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.84 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 29.10 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.32), residues: 704
  helix:  2.15 (0.24), residues: 458
  sheet: -1.19 (0.86), residues: 26
  loop : -0.31 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  47 
 TYR   0.012   0.001   TYR D 660 
 PHE   0.032   0.002   PHE D 718 
 TRP   0.011   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 7928)
  covalent geometry    : angle       0.52175 /  0.28 (11086)
  hydrogen bonds       : bond        0.04018 /  2.65 (  444)
  hydrogen bonds       : angle       4.08658 /  2.83 ( 1207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2394.17 seconds
wall clock time: 41 minutes 39.52 seconds (2499.52 seconds total)