Starting phenix.real_space_refine
on Sun Apr  5 03:07:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rvy_54292/04_2026/9rvy_54292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rvy_54292/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rvy_54292/04_2026/9rvy_54292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rvy_54292/04_2026/9rvy_54292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rvy_54292/04_2026/9rvy_54292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rvy_54292/04_2026/9rvy_54292.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 1.94, 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: 0.81
  Conformation dependent library (CDL) restraints added in 246.1 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: 1.06
  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: 1.35

  Time building geometry restraints manager: 1.06 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=" O   ARG B 724 "
        pdb=" C   ARG B 724 "
        pdb=" N   LEU B 725 "
      ideal   model   delta    sigma   weight residual
     122.12  117.18    4.94 1.06e+00 8.90e-01 2.17e+01
  angle pdb=" CA  ARG D 120 "
        pdb=" C   ARG D 120 "
        pdb=" O   ARG D 120 "
      ideal   model   delta    sigma   weight residual
     119.60  114.23    5.37 1.17e+00 7.31e-01 2.10e+01
  angle pdb=" N   SER C  34 "
        pdb=" CA  SER C  34 "
        pdb=" C   SER C  34 "
      ideal   model   delta    sigma   weight residual
     112.89  107.23    5.66 1.24e+00 6.50e-01 2.08e+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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.860
  Find NCS groups from input model:        0.040
  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:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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= 0.473
  Angle     :  0.756  12.618  11086  Z= 0.437
  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
  covalent geometry    : bond        0.00702 ( 7928)
  covalent geometry    : angle       0.75578 (11086)
  hydrogen bonds       : bond        0.11488 (  444)
  hydrogen bonds       : angle       5.49621 ( 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  : 0.205 
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: 0.6888
  time to fit residues: 77.7450
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  : 0.263 
-------------------------------------------------------------------------------
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:    3.9990
   overall best weight:    1.1682

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

Flipped N/Q/H residues before XYZ refinement:
A 708 GLN
D 714 HIS
C 140 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.184845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.139868 restraints weight = 10552.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.88
r_work: 0.3217 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7928  Z= 0.153
  Angle     :  0.546   6.988  11086  Z= 0.284
  Chirality :  0.037   0.159   1323
  Planarity :  0.004   0.036   1106
  Dihedral  : 16.421 174.106   2055
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.86 %
    Favored  : 74.60 %
  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:  2.11 (0.24), residues: 459
  sheet: -0.86 (0.97), residues: 25
  loop : -0.53 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 730 
 TYR   0.010   0.001   TYR D   6 
 PHE   0.016   0.002   PHE C 104 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7928)
  covalent geometry    : angle       0.54554 (11086)
  hydrogen bonds       : bond        0.04453 (  444)
  hydrogen bonds       : angle       4.36929 ( 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
  123 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.349 
Fit side-chains
REVERT: D  634 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7644 (ttm110)
REVERT: D  710 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7203 (mm)
REVERT: D  714 HIS cc_start: 0.8177 (t-90) cc_final: 0.7929 (t70)
REVERT: D  743 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7828 (ttp)
REVERT: D  798 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: D  801 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7593 (mptt)
REVERT: C   29 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8374 (m)
REVERT: C   46 MET cc_start: 0.8852 (mtp) cc_final: 0.8503 (ptm)
REVERT: C   99 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7249 (mt-10)
REVERT: C  110 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7510 (pp30)
REVERT: C  134 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.8043 (ttp-170)
REVERT: C  149 MET cc_start: 0.6624 (tmm) cc_final: 0.6070 (mmt)
  outliers start: 22
  outliers final: 7
  residues processed: 110
  average time/residue: 0.6364
  time to fit residues: 73.6788
Evaluate side-chains
  103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  710 LEU
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:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 47 optimal weight:    0.2980
   chunk 5 optimal weight:    9.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 706 ASN
C 140 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.187199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.140021 restraints weight = 10594.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.59
r_work: 0.3286 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7928  Z= 0.116
  Angle     :  0.498   7.168  11086  Z= 0.257
  Chirality :  0.034   0.119   1323
  Planarity :  0.004   0.039   1106
  Dihedral  : 16.396 169.045   2051
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.84 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.67 %
    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:  2.06 (0.32), residues: 704
  helix:  2.27 (0.24), residues: 460
  sheet: -0.47 (0.95), residues: 28
  loop : -0.36 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 619 
 TYR   0.010   0.001   TYR D 393 
 PHE   0.019   0.002   PHE D 718 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7928)
  covalent geometry    : angle       0.49833 (11086)
  hydrogen bonds       : bond        0.03853 (  444)
  hydrogen bonds       : angle       4.06831 ( 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
  126 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  634 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7671 (ttm110)
REVERT: D  714 HIS cc_start: 0.8308 (t-90) cc_final: 0.8069 (t70)
REVERT: D  730 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7430 (mtt-85)
REVERT: D  743 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7806 (ttp)
REVERT: D  801 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (mptm)
REVERT: C   29 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8233 (m)
REVERT: C   46 MET cc_start: 0.8873 (mtp) cc_final: 0.8504 (ptp)
REVERT: C  108 MET cc_start: 0.5265 (OUTLIER) cc_final: 0.4437 (tmm)
REVERT: C  110 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7624 (pp30)
REVERT: C  149 MET cc_start: 0.6517 (tmm) cc_final: 0.6059 (mmt)
  outliers start: 23
  outliers final: 11
  residues processed: 112
  average time/residue: 0.6710
  time to fit residues: 78.8240
Evaluate side-chains
  111 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  716 GLN
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
C 140 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.184824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137847 restraints weight = 10629.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.80
r_work: 0.3222 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7928  Z= 0.167
  Angle     :  0.531   7.676  11086  Z= 0.273
  Chirality :  0.035   0.126   1323
  Planarity :  0.004   0.075   1106
  Dihedral  : 16.425 166.343   2051
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.98 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 23.47 %
    Favored  : 72.03 %
  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:  1.84 (0.32), residues: 704
  helix:  2.12 (0.24), residues: 458
  sheet: -0.77 (0.89), residues: 28
  loop : -0.44 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  47 
 TYR   0.016   0.001   TYR D 393 
 PHE   0.015   0.002   PHE C  17 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7928)
  covalent geometry    : angle       0.53064 (11086)
  hydrogen bonds       : bond        0.04300 (  444)
  hydrogen bonds       : angle       4.12824 ( 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
  125 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: D  634 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7699 (ttm110)
REVERT: D  714 HIS cc_start: 0.8253 (t-90) cc_final: 0.8009 (t70)
REVERT: D  801 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7835 (mptm)
REVERT: C   29 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8335 (m)
REVERT: C  108 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.4404 (tmm)
REVERT: C  110 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7553 (pp30)
REVERT: C  149 MET cc_start: 0.6613 (tmm) cc_final: 0.5939 (mmm)
  outliers start: 28
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6455
  time to fit residues: 74.6206
Evaluate side-chains
  106 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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 B residue  738 GLU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  716 GLN
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   73 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
D  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.183890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135940 restraints weight = 10494.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.85
r_work: 0.3207 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7928  Z= 0.180
  Angle     :  0.546   7.720  11086  Z= 0.279
  Chirality :  0.036   0.123   1323
  Planarity :  0.004   0.054   1106
  Dihedral  : 16.541 165.934   2051
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 25.72 %
    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:  1.69 (0.31), residues: 704
  helix:  2.01 (0.24), residues: 458
  sheet: -0.92 (0.88), residues: 28
  loop : -0.50 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  47 
 TYR   0.015   0.001   TYR D 393 
 PHE   0.017   0.002   PHE C  17 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.004   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7928)
  covalent geometry    : angle       0.54597 (11086)
  hydrogen bonds       : bond        0.04443 (  444)
  hydrogen bonds       : angle       4.13936 ( 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: 26
    poor density    : 97
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  744 ARG cc_start: 0.7089 (tpm170) cc_final: 0.6871 (tpm170)
REVERT: D  621 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6103 (p0)
REVERT: D  634 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7532 (ttm110)
REVERT: D  714 HIS cc_start: 0.8236 (t-90) cc_final: 0.7967 (t70)
REVERT: D  801 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7643 (mptt)
REVERT: C   29 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8384 (m)
REVERT: C  108 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4318 (tmm)
REVERT: C  110 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7583 (pp30)
REVERT: C  149 MET cc_start: 0.6617 (tmm) cc_final: 0.5958 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 110
  average time/residue: 0.6518
  time to fit residues: 75.3802
Evaluate side-chains
  112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  709 LEU
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  117 VAL
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  716 GLN
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   73 ASP
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:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 26 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
D  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.185632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.138362 restraints weight = 10617.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.70
r_work: 0.3254 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2395

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= 0.127
  Angle     :  0.506   8.124  11086  Z= 0.259
  Chirality :  0.034   0.127   1323
  Planarity :  0.004   0.041   1106
  Dihedral  : 16.517 164.725   2051
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.70 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.17 %
    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:  1.79 (0.32), residues: 704
  helix:  2.11 (0.24), residues: 459
  sheet: -0.94 (0.88), residues: 28
  loop : -0.51 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  47 
 TYR   0.011   0.001   TYR D 660 
 PHE   0.015   0.002   PHE D 586 
 TRP   0.009   0.001   TRP D 692 
 HIS   0.002   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7928)
  covalent geometry    : angle       0.50613 (11086)
  hydrogen bonds       : bond        0.03921 (  444)
  hydrogen bonds       : angle       3.96287 ( 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
  125 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6877 (p0)
REVERT: D  596 MET cc_start: 0.6373 (mmt) cc_final: 0.6104 (mmt)
REVERT: D  621 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6305 (p0)
REVERT: D  634 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7440 (ttm110)
REVERT: D  714 HIS cc_start: 0.8254 (t-90) cc_final: 0.7989 (t70)
REVERT: D  801 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7618 (mptt)
REVERT: C   29 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8279 (m)
REVERT: C  108 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4484 (tmm)
REVERT: C  110 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7587 (pp30)
REVERT: C  125 HIS cc_start: 0.6203 (m-70) cc_final: 0.5570 (m90)
REVERT: C  149 MET cc_start: 0.6656 (tmm) cc_final: 0.5980 (mmm)
  outliers start: 23
  outliers final: 11
  residues processed: 115
  average time/residue: 0.6393
  time to fit residues: 77.2403
Evaluate side-chains
  112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 ASP
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  117 VAL
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  716 GLN
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   73 ASP
Chi-restraints excluded: chain C residue  108 MET
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:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.186047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.139806 restraints weight = 10552.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.71
r_work: 0.3265 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7928  Z= 0.128
  Angle     :  0.515   9.518  11086  Z= 0.262
  Chirality :  0.034   0.133   1323
  Planarity :  0.004   0.050   1106
  Dihedral  : 16.453 162.350   2051
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.70 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 28.30 %
    Favored  : 68.33 %
  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:  1.86 (0.32), residues: 704
  helix:  2.17 (0.24), residues: 458
  sheet: -1.10 (0.85), residues: 28
  loop : -0.48 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  47 
 TYR   0.011   0.001   TYR D 393 
 PHE   0.013   0.002   PHE C  17 
 TRP   0.009   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7928)
  covalent geometry    : angle       0.51471 (11086)
  hydrogen bonds       : bond        0.03809 (  444)
  hydrogen bonds       : angle       3.91034 ( 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
  121 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6857 (p0)
REVERT: D  160 ASP cc_start: 0.6935 (t70) cc_final: 0.6572 (t0)
REVERT: D  621 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6259 (p0)
REVERT: D  634 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7361 (ttm110)
REVERT: D  714 HIS cc_start: 0.8262 (t-90) cc_final: 0.8011 (t70)
REVERT: D  801 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (mptm)
REVERT: C   29 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8274 (m)
REVERT: C  108 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4633 (tmm)
REVERT: C  110 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7541 (pp30)
REVERT: C  125 HIS cc_start: 0.6365 (m-70) cc_final: 0.5779 (m90)
REVERT: C  149 MET cc_start: 0.6552 (tmm) cc_final: 0.5907 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6176
  time to fit residues: 71.5728
Evaluate side-chains
  113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 ASP
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  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
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  716 GLN
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   73 ASP
Chi-restraints excluded: chain C residue  108 MET
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:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0570
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.8098

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.186163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138886 restraints weight = 10603.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.72
r_work: 0.3262 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7928  Z= 0.127
  Angle     :  0.539   9.310  11086  Z= 0.272
  Chirality :  0.034   0.134   1323
  Planarity :  0.003   0.041   1106
  Dihedral  : 16.424 161.810   2051
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.84 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.46 %
    Favored  : 67.36 %
  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:  1.86 (0.32), residues: 704
  helix:  2.18 (0.24), residues: 458
  sheet: -1.32 (0.82), residues: 28
  loop : -0.46 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  47 
 TYR   0.011   0.001   TYR D 660 
 PHE   0.016   0.002   PHE D 586 
 TRP   0.007   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7928)
  covalent geometry    : angle       0.53917 (11086)
  hydrogen bonds       : bond        0.03790 (  444)
  hydrogen bonds       : angle       3.84067 ( 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
  123 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6858 (p0)
REVERT: D  160 ASP cc_start: 0.6872 (t70) cc_final: 0.6515 (t0)
REVERT: D  621 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6311 (p0)
REVERT: D  634 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7337 (ttm110)
REVERT: D  714 HIS cc_start: 0.8251 (t-90) cc_final: 0.8008 (t70)
REVERT: C   29 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8253 (m)
REVERT: C  105 LYS cc_start: 0.7308 (tptp) cc_final: 0.7003 (ptpp)
REVERT: C  110 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7532 (pp30)
REVERT: C  125 HIS cc_start: 0.6367 (m-70) cc_final: 0.5760 (m90)
  outliers start: 26
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6385
  time to fit residues: 73.7650
Evaluate side-chains
  109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 ASP
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  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
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  716 GLN
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   73 ASP
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:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 59 optimal weight:    0.3980
   chunk 26 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 49 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.186744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.140198 restraints weight = 10633.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.55
r_work: 0.3282 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7928  Z= 0.121
  Angle     :  0.525   8.997  11086  Z= 0.265
  Chirality :  0.034   0.135   1323
  Planarity :  0.004   0.049   1106
  Dihedral  : 16.402 161.142   2051
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 29.26 %
    Favored  : 67.68 %
  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:  1.92 (0.32), residues: 704
  helix:  2.20 (0.24), residues: 459
  sheet: -1.34 (0.81), residues: 28
  loop : -0.36 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  47 
 TYR   0.011   0.001   TYR D 660 
 PHE   0.013   0.002   PHE C 104 
 TRP   0.007   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7928)
  covalent geometry    : angle       0.52534 (11086)
  hydrogen bonds       : bond        0.03704 (  444)
  hydrogen bonds       : angle       3.83271 ( 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
  114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6837 (p0)
REVERT: D  160 ASP cc_start: 0.6867 (t70) cc_final: 0.6502 (t0)
REVERT: D  596 MET cc_start: 0.6599 (mmt) cc_final: 0.6240 (mmm)
REVERT: D  621 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6078 (p0)
REVERT: D  634 ARG cc_start: 0.7746 (mtp-110) cc_final: 0.7270 (ttm110)
REVERT: D  714 HIS cc_start: 0.8247 (t-90) cc_final: 0.8001 (t70)
REVERT: C   29 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8257 (m)
REVERT: C  101 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7262 (tppt)
REVERT: C  105 LYS cc_start: 0.7299 (tptp) cc_final: 0.6976 (ptpp)
REVERT: C  108 MET cc_start: 0.5092 (ttp) cc_final: 0.4273 (tmm)
REVERT: C  110 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7584 (pp30)
REVERT: C  125 HIS cc_start: 0.6386 (m-70) cc_final: 0.6065 (m90)
  outliers start: 19
  outliers final: 11
  residues processed: 106
  average time/residue: 0.6380
  time to fit residues: 70.9336
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  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 ASP
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  117 VAL
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  716 GLN
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   73 ASP
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:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0870
   chunk 76 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.188102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137186 restraints weight = 10676.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.86
r_work: 0.3384 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7928  Z= 0.108
  Angle     :  0.529   9.803  11086  Z= 0.265
  Chirality :  0.034   0.172   1323
  Planarity :  0.004   0.046   1106
  Dihedral  : 16.397 161.178   2051
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.84 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 30.23 %
    Favored  : 67.68 %
  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:  2.02 (0.32), residues: 704
  helix:  2.27 (0.24), residues: 459
  sheet: -1.32 (0.82), residues: 28
  loop : -0.31 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG D 730 
 TYR   0.012   0.001   TYR D 660 
 PHE   0.015   0.002   PHE D 586 
 TRP   0.008   0.001   TRP D 692 
 HIS   0.003   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7928)
  covalent geometry    : angle       0.52897 (11086)
  hydrogen bonds       : bond        0.03505 (  444)
  hydrogen bonds       : angle       3.78115 ( 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
  107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  703 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6879 (p0)
REVERT: D  160 ASP cc_start: 0.6985 (t70) cc_final: 0.6622 (t0)
REVERT: D  596 MET cc_start: 0.6722 (mmt) cc_final: 0.6413 (mmm)
REVERT: D  621 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6099 (p0)
REVERT: D  634 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7353 (ttm110)
REVERT: D  714 HIS cc_start: 0.8258 (t-90) cc_final: 0.8019 (t70)
REVERT: C   29 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8279 (m)
REVERT: C   46 MET cc_start: 0.9002 (mtp) cc_final: 0.8568 (ptp)
REVERT: C  105 LYS cc_start: 0.7369 (tptp) cc_final: 0.7073 (ptpp)
REVERT: C  108 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4302 (tmm)
REVERT: C  110 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7448 (pp30)
REVERT: C  125 HIS cc_start: 0.6520 (m-70) cc_final: 0.5954 (m90)
  outliers start: 13
  outliers final: 7
  residues processed: 102
  average time/residue: 0.6480
  time to fit residues: 69.4034
Evaluate side-chains
  101 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  703 ASP
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  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  716 GLN
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.182600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.134938 restraints weight = 10577.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.48
r_work: 0.3217 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   7928  Z= 0.278
  Angle     :  0.622   9.624  11086  Z= 0.315
  Chirality :  0.039   0.166   1323
  Planarity :  0.005   0.051   1106
  Dihedral  : 16.388 160.636   2051
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.98 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 29.90 %
    Favored  : 67.85 %
  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:  1.45 (0.31), residues: 704
  helix:  1.88 (0.24), residues: 458
  sheet: -1.55 (0.82), residues: 28
  loop : -0.65 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D 730 
 TYR   0.020   0.002   TYR D 393 
 PHE   0.019   0.003   PHE C  17 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 7928)
  covalent geometry    : angle       0.62158 (11086)
  hydrogen bonds       : bond        0.04991 (  444)
  hydrogen bonds       : angle       4.08797 ( 1207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2809.69 seconds
wall clock time: 48 minutes 35.72 seconds (2915.72 seconds total)