Starting phenix.real_space_refine
on Wed Aug  5 00:49:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rvz_54293/08_2026/9rvz_54293.map"
  }
  resolution = 3.2
  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      38      5.16       5
     C    4514      2.51       5
     N    1323      2.21       5
     O    1713      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7676
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 432
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 434
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 3711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3711
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 1249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1249
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 4, 'TRANS': 149}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 2, 'rna3p': 41}
    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: 1.82, per 1000 atoms: 0.24
  Number of scatterers: 7676
  At special positions: 0
  Unit cell: (81.543, 94.251, 154.614, 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      38     16.00
     P      88     15.00
     O    1713      8.00
     N    1323      7.00
     C    4514      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: 0.64
  Conformation dependent library (CDL) restraints added in 342.8 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      69.8% alpha, 6.4% beta
      35 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.603A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.512A  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: 3.724A  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 111
      removed outlier: 3.657A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.794A  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: 4.216A  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 618 through 629
    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: 3.503A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.773A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 688
      removed outlier: 4.045A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.597A  pdb=" N   MET D 702 " --> pdb=" O   THR D 698 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS D 714 " --> pdb=" O   LEU D 710 " (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: 3.932A  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 801
    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 36
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 42 through 50
      removed outlier: 4.110A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 96 through 110
      removed outlier: 3.837A  pdb=" N   GLN C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
      removed outlier: 3.815A  pdb=" N   LEU C 122 " --> pdb=" O   PRO C 118 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (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: 3.641A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   PHE D 637 " --> pdb=" O   VAL D 611 " (cutoff:3.500A)
      removed outlier: 6.420A  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.
    1074 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      74 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1121
        1.32 -     1.44: 2503
        1.44 -     1.56: 4115
        1.56 -     1.69: 174
        1.69 -     1.81: 63
  Bond restraints: 7976
  Sorted by residual:
  bond pdb=" CA  ASP D 617 "
       pdb=" C   ASP D 617 "
    ideal  model  delta    sigma   weight residual
    1.532  1.477  0.055 9.60e-03 1.09e+04 3.31e+01
  bond pdb=" CA  HIS C  31 "
       pdb=" C   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.523  1.456  0.067 1.37e-02 5.33e+03 2.40e+01
  bond pdb=" CA  ASP D 617 "
       pdb=" CB  ASP D 617 "
    ideal  model  delta    sigma   weight residual
    1.533  1.478  0.056 1.37e-02 5.33e+03 1.64e+01
  bond pdb=" N   ASP D 617 "
       pdb=" CA  ASP D 617 "
    ideal  model  delta    sigma   weight residual
    1.462  1.413  0.049 1.31e-02 5.83e+03 1.40e+01
  bond pdb=" C   TYR D  74 "
       pdb=" N   VAL D  75 "
    ideal  model  delta    sigma   weight residual
    1.331  1.384 -0.053 1.43e-02 4.89e+03 1.40e+01
  ... (remaining 7971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 11060
        3.19 -     6.38: 79
        6.38 -     9.57: 0
        9.57 -    12.76: 1
       12.76 -    15.95: 1
  Bond angle restraints: 11141
  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
     109.50  125.45  -15.95 2.20e+00 2.07e-01 5.26e+01
  angle pdb=" O4'   C E  33 "
        pdb=" C4'   C E  33 "
        pdb=" C3'   C E  33 "
      ideal   model   delta    sigma   weight residual
     106.10  100.72    5.38 8.00e-01 1.56e+00 4.52e+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  114.69    3.91 6.00e-01 2.78e+00 4.25e+01
  angle pdb=" N6    A F  38 "
        pdb=" C6    A F  38 "
        pdb=" N1    A F  38 "
      ideal   model   delta    sigma   weight residual
     118.60  115.10    3.50 6.00e-01 2.78e+00 3.40e+01
  angle pdb=" N6    A F  21 "
        pdb=" C6    A F  21 "
        pdb=" N1    A F  21 "
      ideal   model   delta    sigma   weight residual
     118.60  115.16    3.44 6.00e-01 2.78e+00 3.29e+01
  ... (remaining 11136 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.17: 4647
       35.17 -    70.35: 248
       70.35 -   105.52: 22
      105.52 -   140.70: 0
      140.70 -   175.87: 2
  Dihedral angle restraints: 4919
    sinusoidal: 2799
      harmonic: 2120
  Sorted by residual:
  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
     147.00   55.43   91.57     1      8.00e+00 1.56e-02 1.54e+02
  dihedral pdb=" O4'   C E  33 "
           pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" C2'   C E  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -44.23   68.23     1      8.00e+00 1.56e-02 9.44e+01
  dihedral pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" C2'   C E  33 "
           pdb=" C1'   C E  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   32.20  -67.20     1      8.00e+00 1.56e-02 9.19e+01
  ... (remaining 4916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 1313
       0.161 -    0.321: 8
       0.321 -    0.482: 1
       0.482 -    0.642: 0
       0.642 -    0.803: 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     -2.74   -1.94   -0.80 2.00e-01 2.50e+01 1.61e+01
  chirality pdb=" CA  GLN D 683 "
            pdb=" N   GLN D 683 "
            pdb=" C   GLN D 683 "
            pdb=" CB  GLN D 683 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  ASP D 617 "
            pdb=" N   ASP D 617 "
            pdb=" C   ASP D 617 "
            pdb=" CB  ASP D 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1320 not shown)

  Planarity restraints: 1112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  17 "    0.079 2.00e-02 2.50e+03   3.21e-02 2.83e+01
        pdb=" N9    A F  17 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8    A F  17 "   -0.024 2.00e-02 2.50e+03
        pdb=" N7    A F  17 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    A F  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    A F  17 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A F  17 "    0.045 2.00e-02 2.50e+03
        pdb=" N1    A F  17 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A F  17 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3    A F  17 "   -0.016 2.00e-02 2.50e+03
        pdb=" C4    A F  17 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F   1 "   -0.059 2.00e-02 2.50e+03   2.80e-02 1.77e+01
        pdb=" N1    C F   1 "    0.036 2.00e-02 2.50e+03
        pdb=" C2    C F   1 "    0.012 2.00e-02 2.50e+03
        pdb=" O2    C F   1 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    C F   1 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C F   1 "    0.008 2.00e-02 2.50e+03
        pdb=" N4    C F   1 "   -0.039 2.00e-02 2.50e+03
        pdb=" C5    C F   1 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    C F   1 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F  11 "   -0.055 2.00e-02 2.50e+03   2.55e-02 1.46e+01
        pdb=" N1    U F  11 "    0.040 2.00e-02 2.50e+03
        pdb=" C2    U F  11 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    U F  11 "    0.016 2.00e-02 2.50e+03
        pdb=" N3    U F  11 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    U F  11 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U F  11 "   -0.021 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
  ... (remaining 1109 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 460
        2.72 -     3.27: 7668
        3.27 -     3.81: 13304
        3.81 -     4.36: 15846
        4.36 -     4.90: 25233
  Nonbonded interactions: 62511
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 589 "
            pdb=" OG  SER D 592 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O2'   C E  36 "
            pdb=" OP1   A E  38 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" N   GLU D 116 "
            pdb=" OE1 GLU D 116 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" O   GLU A 696 "
            pdb=" OG1 THR A 700 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" O   ASN D 566 "
            pdb=" OD1 ASN D 566 "
     model   vdw
     2.376 3.040
  ... (remaining 62506 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 695 through 699 or (resid 700 through 701 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 702 through 747))
  selection = (chain 'B' and (resid 695 through 700 or (resid 701 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 702 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:             1.270
  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:                    0.010
  Process input model:                     8.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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      :  0.004   0.067   7976  Z= 0.355
  Angle     :  0.765  15.955  11141  Z= 0.713
  Chirality :  0.054   0.803   1323
  Planarity :  0.004   0.032   1112
  Dihedral  : 18.971 175.872   3543
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 17.56 %
    Favored  : 82.12 %
  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: 706
  helix:  2.08 (0.24), residues: 448
  sheet:  0.52 (1.12), residues: 26
  loop : -0.34 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 126 
 TYR   0.008   0.001   TYR D 103 
 PHE   0.014   0.001   PHE C 104 
 TRP   0.002   0.001   TRP D 522 
 HIS   0.009   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.36 ( 7976)
  covalent geometry    : angle       0.76523 /  0.71 (11141)
  hydrogen bonds       : bond        0.11228 /  7.86 (  446)
  hydrogen bonds       : angle       5.16427 /  3.73 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.8297 (tmm) cc_final: 0.7975 (tmm)
REVERT: A  742 MET cc_start: 0.6777 (tmm) cc_final: 0.6549 (tmm)
REVERT: A  745 GLU cc_start: 0.5309 (tt0) cc_final: 0.5105 (tm-30)
REVERT: D  617 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8379 (t70)
REVERT: D  768 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: C   44 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8370 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0822
  time to fit residues: 13.2785
Evaluate side-chains
  103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  617 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.4042

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 721 GLN
D 128 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.112929 restraints weight = 13643.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.39
r_work: 0.3405 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7976  Z= 0.128
  Angle     :  0.538  10.973  11141  Z= 0.310
  Chirality :  0.040   0.645   1323
  Planarity :  0.004   0.033   1112
  Dihedral  : 16.471 167.929   2055
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 18.20 %
    Favored  : 80.70 %
  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 (0.31), residues: 706
  helix:  2.09 (0.24), residues: 455
  sheet:  0.08 (1.01), residues: 27
  loop : -0.30 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 736 
 TYR   0.008   0.001   TYR D 103 
 PHE   0.033   0.002   PHE C 104 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 616 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.13 ( 7976)
  covalent geometry    : angle       0.53792 /  0.31 (11141)
  hydrogen bonds       : bond        0.05100 /  3.45 (  446)
  hydrogen bonds       : angle       4.29305 /  3.13 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 GLU cc_start: 0.5187 (tt0) cc_final: 0.4912 (tm-30)
REVERT: B  743 ASP cc_start: 0.6581 (t70) cc_final: 0.6376 (t70)
REVERT: D   12 MET cc_start: 0.8674 (mmm) cc_final: 0.8420 (mmm)
REVERT: D  768 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: C   19 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8049 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 112
  average time/residue: 0.0907
  time to fit residues: 13.4674
Evaluate side-chains
  104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0010
   chunk 13 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.149416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111623 restraints weight = 13759.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.44
r_work: 0.3385 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7976  Z= 0.132
  Angle     :  0.512   8.043  11141  Z= 0.289
  Chirality :  0.040   0.660   1323
  Planarity :  0.004   0.037   1112
  Dihedral  : 16.438 173.293   2053
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.51 %
    Favored  : 78.64 %
  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:  1.99 (0.31), residues: 706
  helix:  2.17 (0.24), residues: 458
  sheet:  0.33 (0.97), residues: 25
  loop : -0.35 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 699 
 TYR   0.016   0.001   TYR D 393 
 PHE   0.024   0.002   PHE C 104 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 7976)
  covalent geometry    : angle       0.51206 /  0.29 (11141)
  hydrogen bonds       : bond        0.04657 /  3.12 (  446)
  hydrogen bonds       : angle       4.15717 /  3.05 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 GLU cc_start: 0.5092 (tt0) cc_final: 0.4869 (tm-30)
REVERT: D   12 MET cc_start: 0.8698 (mmm) cc_final: 0.8443 (mmm)
REVERT: D  748 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (m-40)
  outliers start: 18
  outliers final: 12
  residues processed: 113
  average time/residue: 0.0927
  time to fit residues: 14.1121
Evaluate side-chains
  110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  710 LEU
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  718 PHE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  748 ASN
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0070
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7402

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.148964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.112391 restraints weight = 14085.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.35
r_work: 0.3422 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7976  Z= 0.114
  Angle     :  0.473   8.604  11141  Z= 0.268
  Chirality :  0.038   0.615   1323
  Planarity :  0.003   0.036   1112
  Dihedral  : 16.456 173.878   2053
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.83 %
    Favored  : 78.01 %
  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 (0.31), residues: 706
  helix:  2.12 (0.24), residues: 459
  sheet:  0.18 (0.97), residues: 25
  loop : -0.28 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 699 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.037   0.002   PHE C 104 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 7976)
  covalent geometry    : angle       0.47276 /  0.27 (11141)
  hydrogen bonds       : bond        0.04363 /  2.93 (  446)
  hydrogen bonds       : angle       4.02914 /  2.96 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 GLU cc_start: 0.5177 (tt0) cc_final: 0.4790 (tm-30)
REVERT: B  737 LEU cc_start: 0.8334 (tp) cc_final: 0.8129 (tp)
REVERT: B  747 ARG cc_start: 0.5948 (ttm170) cc_final: 0.5727 (mtt180)
REVERT: D   12 MET cc_start: 0.8570 (mmm) cc_final: 0.8334 (mmm)
REVERT: D  748 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8043 (m-40)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.0824
  time to fit residues: 13.0261
Evaluate side-chains
  112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  710 LEU
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  748 ASN
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 44 optimal weight:    0.0060
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.149137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114214 restraints weight = 13948.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.17
r_work: 0.3420 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7976  Z= 0.109
  Angle     :  0.475   8.946  11141  Z= 0.265
  Chirality :  0.037   0.596   1323
  Planarity :  0.003   0.035   1112
  Dihedral  : 16.463 176.776   2053
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.78 %
    Favored  : 77.37 %
  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 (0.31), residues: 706
  helix:  2.19 (0.24), residues: 460
  sheet:  0.09 (0.96), residues: 25
  loop : -0.31 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 699 
 TYR   0.008   0.001   TYR D 103 
 PHE   0.025   0.002   PHE C 104 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.11 ( 7976)
  covalent geometry    : angle       0.47493 /  0.26 (11141)
  hydrogen bonds       : bond        0.04176 /  2.80 (  446)
  hydrogen bonds       : angle       3.93977 /  2.89 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  706 ASN cc_start: 0.8202 (t0) cc_final: 0.7995 (t0)
REVERT: A  745 GLU cc_start: 0.5020 (tt0) cc_final: 0.4642 (tm-30)
REVERT: B  737 LEU cc_start: 0.8392 (tp) cc_final: 0.8186 (tp)
REVERT: D   12 MET cc_start: 0.8525 (mmm) cc_final: 0.8306 (mmm)
REVERT: D  386 GLU cc_start: 0.5195 (tp30) cc_final: 0.4913 (tp30)
REVERT: D  596 MET cc_start: 0.8521 (ttm) cc_final: 0.8233 (mtt)
REVERT: D  748 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (m-40)
REVERT: C   45 GLU cc_start: 0.7394 (tp30) cc_final: 0.7162 (tp30)
  outliers start: 18
  outliers final: 13
  residues processed: 118
  average time/residue: 0.0814
  time to fit residues: 12.9290
Evaluate side-chains
  113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  710 LEU
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  748 ASN
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 608 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.147694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.111138 restraints weight = 13985.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.34
r_work: 0.3392 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7976  Z= 0.132
  Angle     :  0.493  10.541  11141  Z= 0.270
  Chirality :  0.038   0.592   1323
  Planarity :  0.003   0.035   1112
  Dihedral  : 16.466 177.253   2053
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.73 %
    Favored  : 75.95 %
  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:  2.08 (0.31), residues: 706
  helix:  2.24 (0.24), residues: 458
  sheet: -0.01 (0.94), residues: 25
  loop : -0.26 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 699 
 TYR   0.010   0.001   TYR D 704 
 PHE   0.022   0.002   PHE C 104 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 7976)
  covalent geometry    : angle       0.49322 /  0.27 (11141)
  hydrogen bonds       : bond        0.04353 /  2.90 (  446)
  hydrogen bonds       : angle       3.96349 /  2.92 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  706 ASN cc_start: 0.8218 (t0) cc_final: 0.7997 (t0)
REVERT: A  745 GLU cc_start: 0.5014 (tt0) cc_final: 0.4654 (tm-30)
REVERT: B  747 ARG cc_start: 0.5946 (ttm170) cc_final: 0.5718 (mtt180)
REVERT: D   12 MET cc_start: 0.8535 (mmm) cc_final: 0.8314 (mmm)
REVERT: D  556 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8224 (pt)
REVERT: D  596 MET cc_start: 0.8517 (ttm) cc_final: 0.8234 (mtt)
REVERT: C   45 GLU cc_start: 0.7505 (tp30) cc_final: 0.7274 (tp30)
  outliers start: 21
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0781
  time to fit residues: 12.2715
Evaluate side-chains
  118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  556 ILE
Chi-restraints excluded: chain D residue  559 SER
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 78 optimal weight:   30.0000
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 701 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.149170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.112938 restraints weight = 13954.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.24
r_work: 0.3406 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7976  Z= 0.118
  Angle     :  0.500  14.530  11141  Z= 0.271
  Chirality :  0.038   0.594   1323
  Planarity :  0.003   0.034   1112
  Dihedral  : 16.516 177.030   2053
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 20.89 %
    Favored  : 75.16 %
  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:  2.10 (0.31), residues: 706
  helix:  2.25 (0.24), residues: 459
  sheet: -0.32 (0.91), residues: 25
  loop : -0.20 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG D 699 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.022   0.002   PHE C 104 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.002   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 7976)
  covalent geometry    : angle       0.50038 /  0.27 (11141)
  hydrogen bonds       : bond        0.04178 /  2.78 (  446)
  hydrogen bonds       : angle       3.89641 /  2.88 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  706 ASN cc_start: 0.8202 (t0) cc_final: 0.7982 (t0)
REVERT: A  745 GLU cc_start: 0.5105 (tt0) cc_final: 0.4694 (tm-30)
REVERT: D   12 MET cc_start: 0.8557 (mmm) cc_final: 0.8334 (mmm)
REVERT: D  556 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8159 (pt)
REVERT: D  596 MET cc_start: 0.8429 (ttm) cc_final: 0.8192 (mtt)
REVERT: D  748 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8029 (m-40)
REVERT: C   45 GLU cc_start: 0.7514 (tp30) cc_final: 0.7269 (tp30)
  outliers start: 25
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0813
  time to fit residues: 13.3441
Evaluate side-chains
  118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  556 ILE
Chi-restraints excluded: chain D residue  559 SER
Chi-restraints excluded: chain D residue  577 GLU
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  748 ASN
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  101 LYS
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 78 optimal weight:   30.0000
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0470
   overall best weight:    0.7678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 701 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.113148 restraints weight = 13884.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.36
r_work: 0.3417 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7976  Z= 0.116
  Angle     :  0.499  14.588  11141  Z= 0.269
  Chirality :  0.037   0.597   1323
  Planarity :  0.003   0.033   1112
  Dihedral  : 16.522 175.631   2053
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.36 %
    Favored  : 74.84 %
  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:  2.12 (0.31), residues: 706
  helix:  2.26 (0.24), residues: 459
  sheet: -0.45 (0.90), residues: 25
  loop : -0.18 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG D 699 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.022   0.002   PHE C 104 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 7976)
  covalent geometry    : angle       0.49932 /  0.27 (11141)
  hydrogen bonds       : bond        0.04157 /  2.78 (  446)
  hydrogen bonds       : angle       3.86993 /  2.86 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  706 ASN cc_start: 0.8209 (t0) cc_final: 0.7991 (t0)
REVERT: A  745 GLU cc_start: 0.5107 (tt0) cc_final: 0.4709 (tm-30)
REVERT: D   12 MET cc_start: 0.8507 (mmm) cc_final: 0.8277 (mmm)
REVERT: D  556 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8304 (pt)
REVERT: D  596 MET cc_start: 0.8410 (ttm) cc_final: 0.8181 (mtt)
REVERT: D  679 ASP cc_start: 0.7261 (t0) cc_final: 0.6979 (t70)
REVERT: C   45 GLU cc_start: 0.7552 (tp30) cc_final: 0.7305 (tp30)
  outliers start: 24
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0804
  time to fit residues: 13.3947
Evaluate side-chains
  120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  556 ILE
Chi-restraints excluded: chain D residue  559 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0070
   chunk 23 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 701 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.149518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.113146 restraints weight = 13897.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.33
r_work: 0.3418 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7976  Z= 0.115
  Angle     :  0.506  14.813  11141  Z= 0.272
  Chirality :  0.037   0.595   1323
  Planarity :  0.003   0.032   1112
  Dihedral  : 16.529 174.080   2053
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.15 %
    Favored  : 75.16 %
  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:  2.04 (0.31), residues: 706
  helix:  2.19 (0.24), residues: 459
  sheet: -0.43 (0.92), residues: 25
  loop : -0.19 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D 699 
 TYR   0.009   0.001   TYR B 698 
 PHE   0.021   0.002   PHE C 104 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 7976)
  covalent geometry    : angle       0.50583 /  0.27 (11141)
  hydrogen bonds       : bond        0.04129 /  2.75 (  446)
  hydrogen bonds       : angle       3.87831 /  2.87 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  706 ASN cc_start: 0.8216 (t0) cc_final: 0.7997 (t0)
REVERT: A  745 GLU cc_start: 0.5161 (tt0) cc_final: 0.4764 (tm-30)
REVERT: D   12 MET cc_start: 0.8511 (mmm) cc_final: 0.8286 (mmm)
REVERT: D  556 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8144 (pt)
REVERT: D  596 MET cc_start: 0.8366 (ttm) cc_final: 0.8160 (mtt)
REVERT: D  679 ASP cc_start: 0.7261 (t0) cc_final: 0.6972 (t70)
REVERT: C   45 GLU cc_start: 0.7561 (tp30) cc_final: 0.7325 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 113
  average time/residue: 0.0857
  time to fit residues: 13.4389
Evaluate side-chains
  115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  556 ILE
Chi-restraints excluded: chain D residue  559 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 78 optimal weight:   20.0000
   chunk 33 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.148608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.112005 restraints weight = 13858.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.32
r_work: 0.3407 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7976  Z= 0.134
  Angle     :  0.519  14.101  11141  Z= 0.278
  Chirality :  0.038   0.571   1323
  Planarity :  0.003   0.036   1112
  Dihedral  : 16.463 170.173   2053
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.31 %
    Favored  : 75.16 %
  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:  2.03 (0.31), residues: 706
  helix:  2.20 (0.24), residues: 458
  sheet: -0.61 (0.91), residues: 25
  loop : -0.19 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG D 699 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.020   0.002   PHE C 104 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 7976)
  covalent geometry    : angle       0.51903 /  0.28 (11141)
  hydrogen bonds       : bond        0.04271 /  2.84 (  446)
  hydrogen bonds       : angle       3.90569 /  2.89 ( 1214)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  745 GLU cc_start: 0.5169 (tt0) cc_final: 0.4783 (tm-30)
REVERT: D   12 MET cc_start: 0.8509 (mmm) cc_final: 0.8273 (mmm)
REVERT: D  679 ASP cc_start: 0.7359 (t0) cc_final: 0.7088 (t70)
REVERT: C   45 GLU cc_start: 0.7562 (tp30) cc_final: 0.7322 (tp30)
  outliers start: 16
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0829
  time to fit residues: 12.8032
Evaluate side-chains
  120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  537 LYS
Chi-restraints excluded: chain D residue  559 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  621 ASP
Chi-restraints excluded: chain D residue  713 ILE
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  160 ASP
Chi-restraints excluded: chain C residue  163 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 77 optimal weight:   30.0000
   chunk 59 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.149940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114474 restraints weight = 13691.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.20
r_work: 0.3409 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7976  Z= 0.123
  Angle     :  0.518  14.697  11141  Z= 0.278
  Chirality :  0.037   0.531   1323
  Planarity :  0.003   0.037   1112
  Dihedral  : 16.429 164.714   2053
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.78 %
    Favored  : 75.00 %
  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:  1.97 (0.31), residues: 706
  helix:  2.17 (0.24), residues: 458
  sheet: -1.14 (0.89), residues: 27
  loop : -0.17 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 699 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.016   0.002   PHE C 144 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 7976)
  covalent geometry    : angle       0.51841 /  0.28 (11141)
  hydrogen bonds       : bond        0.04160 /  2.76 (  446)
  hydrogen bonds       : angle       3.87191 /  2.87 ( 1214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.01 seconds
wall clock time: 31 minutes 16.37 seconds (1876.37 seconds total)