Starting phenix.real_space_refine
on Mon Jan 20 21:08:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vgl_43204/01_2025/8vgl_43204.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   1.000
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: 4
    Type Number    sf(0)   Gaussians
     S      92      5.16       5
     C   10188      2.51       5
     N    2496      2.21       5
     O    2846      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 15622
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2239
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
    Chain: "B"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2239
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
    Chain: "C"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2239
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
    Chain: "D"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2239
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
    Chain: "H"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1685
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210}
    Chain: "L"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1648
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204}
    Chain: "F"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1648
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204}
    Chain: "E"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1685
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210}
  Time building chain proxies: 9.51, per 1000 atoms: 0.61
  Number of scatterers: 15622
  At special positions: 0
  Unit cell: (105.734, 107.605, 185.269, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      92     16.00
     O    2846      8.00
     N    2496      7.00
     C   10188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 132 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 134 " - pdb=" SG  CYS F 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 214 " - pdb=" SG  CYS E 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 144 " - pdb=" SG  CYS E 199 " distance=2.03

  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: 3.71
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3716

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 22 sheets defined
      56.3% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1490 through 1502
      removed outlier: 3.792A  pdb=" N   TYR A1494 " --> pdb=" O   GLY A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1503 through 1524
      removed outlier: 3.566A  pdb=" N   VAL A1523 " --> pdb=" O   VAL A1519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1559
      removed outlier: 3.548A  pdb=" N   GLU A1550 " --> pdb=" O   LEU A1546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1560 through 1564
      removed outlier: 3.859A  pdb=" N   PHE A1563 " --> pdb=" O   ILE A1560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1565 through 1584
      removed outlier: 3.626A  pdb=" N   MET A1582 " --> pdb=" O   SER A1578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1584 through 1590
    Processing helix  chain 'A' and resid 1596 through 1601
    Processing helix  chain 'A' and resid 1602 through 1616
      removed outlier: 3.596A  pdb=" N   ARG A1608 " --> pdb=" O   ALA A1604 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   LEU A1612 " --> pdb=" O   ARG A1608 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL A1613 " --> pdb=" O   ILE A1609 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL A1616 " --> pdb=" O   LEU A1612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1616 through 1656
      removed outlier: 3.791A  pdb=" N   ILE A1630 " --> pdb=" O   LEU A1626 " (cutoff:3.500A)
      Proline residue:  A1631  - end of helix
      removed outlier: 4.984A  pdb=" N   SER A1635 " --> pdb=" O   PRO A1631 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   VAL A1636 " --> pdb=" O   GLY A1632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1659 through 1664
    Processing helix  chain 'A' and resid 1665 through 1678
    Processing helix  chain 'A' and resid 1686 through 1692
    Processing helix  chain 'A' and resid 1693 through 1696
      removed outlier: 6.607A  pdb=" N   TYR A1696 " --> pdb=" O   VAL A1693 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1693 through 1696'
    Processing helix  chain 'A' and resid 1697 through 1751
      Proline residue:  A1703  - end of helix
      removed outlier: 3.959A  pdb=" N   LYS A1730 " --> pdb=" O   ILE A1726 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU A1749 " --> pdb=" O   ASN A1745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1751 through 1756
      removed outlier: 4.054A  pdb=" N   GLU A1755 " --> pdb=" O   ILE A1751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1757 through 1759
      No H-bonds generated for 'chain 'A' and resid 1757 through 1759'
    Processing helix  chain 'B' and resid 1489 through 1489
      No H-bonds generated for 'chain 'B' and resid 1489 through 1489'
    Processing helix  chain 'B' and resid 1490 through 1502
      removed outlier: 3.627A  pdb=" N   TYR B1494 " --> pdb=" O   GLY B1490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1503 through 1524
      removed outlier: 3.602A  pdb=" N   VAL B1523 " --> pdb=" O   VAL B1519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1529 through 1559
      removed outlier: 3.544A  pdb=" N   GLU B1550 " --> pdb=" O   LEU B1546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1560 through 1562
      No H-bonds generated for 'chain 'B' and resid 1560 through 1562'
    Processing helix  chain 'B' and resid 1565 through 1584
      removed outlier: 3.919A  pdb=" N   MET B1582 " --> pdb=" O   SER B1578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1584 through 1590
    Processing helix  chain 'B' and resid 1594 through 1601
      removed outlier: 3.921A  pdb=" N   PHE B1598 " --> pdb=" O   SER B1594 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG B1599 " --> pdb=" O   PRO B1595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1602 through 1616
      removed outlier: 3.514A  pdb=" N   ARG B1608 " --> pdb=" O   ALA B1604 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU B1612 " --> pdb=" O   ARG B1608 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   VAL B1613 " --> pdb=" O   ILE B1609 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL B1616 " --> pdb=" O   LEU B1612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1616 through 1656
      removed outlier: 3.766A  pdb=" N   ILE B1630 " --> pdb=" O   LEU B1626 " (cutoff:3.500A)
      Proline residue:  B1631  - end of helix
      removed outlier: 4.984A  pdb=" N   SER B1635 " --> pdb=" O   PRO B1631 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   VAL B1636 " --> pdb=" O   GLY B1632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1659 through 1664
    Processing helix  chain 'B' and resid 1665 through 1678
    Processing helix  chain 'B' and resid 1686 through 1692
    Processing helix  chain 'B' and resid 1693 through 1696
      removed outlier: 6.641A  pdb=" N   TYR B1696 " --> pdb=" O   VAL B1693 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1693 through 1696'
    Processing helix  chain 'B' and resid 1697 through 1757
      Proline residue:  B1703  - end of helix
      removed outlier: 3.863A  pdb=" N   LYS B1730 " --> pdb=" O   ILE B1726 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   GLU B1749 " --> pdb=" O   ASN B1745 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG B1754 " --> pdb=" O   ILE B1750 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLU B1755 " --> pdb=" O   ILE B1751 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1758 through 1759
      No H-bonds generated for 'chain 'B' and resid 1758 through 1759'
    Processing helix  chain 'C' and resid 1489 through 1489
      No H-bonds generated for 'chain 'C' and resid 1489 through 1489'
    Processing helix  chain 'C' and resid 1490 through 1502
      removed outlier: 3.734A  pdb=" N   TYR C1494 " --> pdb=" O   GLY C1490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1503 through 1524
      removed outlier: 3.551A  pdb=" N   VAL C1523 " --> pdb=" O   VAL C1519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1529 through 1559
      removed outlier: 3.544A  pdb=" N   GLU C1550 " --> pdb=" O   LEU C1546 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1560 through 1564
      removed outlier: 3.865A  pdb=" N   PHE C1563 " --> pdb=" O   ILE C1560 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1565 through 1584
      removed outlier: 3.617A  pdb=" N   MET C1582 " --> pdb=" O   SER C1578 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1584 through 1590
    Processing helix  chain 'C' and resid 1596 through 1601
    Processing helix  chain 'C' and resid 1602 through 1616
      removed outlier: 3.593A  pdb=" N   ARG C1608 " --> pdb=" O   ALA C1604 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU C1612 " --> pdb=" O   ARG C1608 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL C1613 " --> pdb=" O   ILE C1609 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL C1616 " --> pdb=" O   LEU C1612 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1616 through 1656
      removed outlier: 3.791A  pdb=" N   ILE C1630 " --> pdb=" O   LEU C1626 " (cutoff:3.500A)
      Proline residue:  C1631  - end of helix
      removed outlier: 4.982A  pdb=" N   SER C1635 " --> pdb=" O   PRO C1631 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   VAL C1636 " --> pdb=" O   GLY C1632 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1659 through 1664
    Processing helix  chain 'C' and resid 1665 through 1678
    Processing helix  chain 'C' and resid 1686 through 1692
    Processing helix  chain 'C' and resid 1693 through 1696
      removed outlier: 6.642A  pdb=" N   TYR C1696 " --> pdb=" O   VAL C1693 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1693 through 1696'
    Processing helix  chain 'C' and resid 1697 through 1751
      Proline residue:  C1703  - end of helix
      removed outlier: 3.881A  pdb=" N   LYS C1730 " --> pdb=" O   ILE C1726 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU C1749 " --> pdb=" O   ASN C1745 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1751 through 1756
      removed outlier: 4.090A  pdb=" N   GLU C1755 " --> pdb=" O   ILE C1751 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1757 through 1759
      No H-bonds generated for 'chain 'C' and resid 1757 through 1759'
    Processing helix  chain 'D' and resid 1489 through 1489
      No H-bonds generated for 'chain 'D' and resid 1489 through 1489'
    Processing helix  chain 'D' and resid 1490 through 1502
      removed outlier: 3.626A  pdb=" N   TYR D1494 " --> pdb=" O   GLY D1490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1503 through 1524
      removed outlier: 3.596A  pdb=" N   VAL D1523 " --> pdb=" O   VAL D1519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1529 through 1559
      removed outlier: 3.536A  pdb=" N   GLU D1550 " --> pdb=" O   LEU D1546 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1560 through 1562
      No H-bonds generated for 'chain 'D' and resid 1560 through 1562'
    Processing helix  chain 'D' and resid 1565 through 1584
      removed outlier: 3.944A  pdb=" N   MET D1582 " --> pdb=" O   SER D1578 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1584 through 1590
    Processing helix  chain 'D' and resid 1596 through 1601
    Processing helix  chain 'D' and resid 1602 through 1616
      removed outlier: 3.513A  pdb=" N   ARG D1608 " --> pdb=" O   ALA D1604 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU D1612 " --> pdb=" O   ARG D1608 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL D1613 " --> pdb=" O   ILE D1609 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL D1616 " --> pdb=" O   LEU D1612 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1616 through 1656
      removed outlier: 3.765A  pdb=" N   ILE D1630 " --> pdb=" O   LEU D1626 " (cutoff:3.500A)
      Proline residue:  D1631  - end of helix
      removed outlier: 4.988A  pdb=" N   SER D1635 " --> pdb=" O   PRO D1631 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   VAL D1636 " --> pdb=" O   GLY D1632 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1659 through 1664
    Processing helix  chain 'D' and resid 1665 through 1678
    Processing helix  chain 'D' and resid 1686 through 1692
    Processing helix  chain 'D' and resid 1693 through 1696
      removed outlier: 6.648A  pdb=" N   TYR D1696 " --> pdb=" O   VAL D1693 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1693 through 1696'
    Processing helix  chain 'D' and resid 1697 through 1757
      Proline residue:  D1703  - end of helix
      removed outlier: 3.900A  pdb=" N   LYS D1730 " --> pdb=" O   ILE D1726 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   GLU D1749 " --> pdb=" O   ASN D1745 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG D1754 " --> pdb=" O   ILE D1750 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU D1755 " --> pdb=" O   ILE D1751 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'H' and resid 188 through 192
    Processing helix  chain 'H' and resid 204 through 207
    Processing helix  chain 'L' and resid 29 through 31
      No H-bonds generated for 'chain 'L' and resid 29 through 31'
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 183 through 188
    Processing helix  chain 'F' and resid 29 through 31
      No H-bonds generated for 'chain 'F' and resid 29 through 31'
    Processing helix  chain 'F' and resid 79 through 83
    Processing helix  chain 'F' and resid 121 through 127
    Processing helix  chain 'F' and resid 183 through 188
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 83 through 87
    Processing helix  chain 'E' and resid 160 through 162
      No H-bonds generated for 'chain 'E' and resid 160 through 162'
    Processing helix  chain 'E' and resid 188 through 192
    Processing helix  chain 'E' and resid 204 through 207
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.021A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   MET H  34 " --> pdb=" O   THR H  50 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.021A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128
      removed outlier: 3.843A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   TYR H 179 " --> pdb=" O   GLY H 148 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   THR H 180 " --> pdb=" O   ALA H 172 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ALA H 172 " --> pdb=" O   THR H 180 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER H 182 " --> pdb=" O   PHE H 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
      removed outlier: 5.263A  pdb=" N   THR L  69 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
      removed outlier: 9.442A  pdb=" N   LEU L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   SER L  67 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 12.001A  pdb=" N   ILE L  28 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 12.148A  pdb=" N   SER L  65 " --> pdb=" O   ILE L  28 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.104A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   TRP L  35 " --> pdb=" O   TRP L  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.104A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.653A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 144 through 145
    Processing sheet with id=AB2, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.624A  pdb=" N   SER L 153 " --> pdb=" O   ILE L 150 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 7
      removed outlier: 5.255A  pdb=" N   THR F  69 " --> pdb=" O   VAL F  25 " (cutoff:3.500A)
      removed outlier: 9.440A  pdb=" N   LEU F  27 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   SER F  67 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 12.001A  pdb=" N   ILE F  28 " --> pdb=" O   SER F  65 " (cutoff:3.500A)
      removed outlier: 12.145A  pdb=" N   SER F  65 " --> pdb=" O   ILE F  28 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.207A  pdb=" N   MET F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TRP F  35 " --> pdb=" O   TRP F  47 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.207A  pdb=" N   MET F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 118
      removed outlier: 5.662A  pdb=" N   TYR F 173 " --> pdb=" O   ASN F 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 145
    Processing sheet with id=AB8, first strand: chain 'F' and resid 153 through 154
      removed outlier: 3.631A  pdb=" N   SER F 153 " --> pdb=" O   ILE F 150 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.049A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   MET E  34 " --> pdb=" O   THR E  50 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   THR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.049A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR E 102 " --> pdb=" O   ARG E  94 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 128
      removed outlier: 3.840A  pdb=" N   GLY E 143 " --> pdb=" O   LEU E 128 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   TYR E 179 " --> pdb=" O   GLY E 148 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   THR E 180 " --> pdb=" O   ALA E 172 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ALA E 172 " --> pdb=" O   THR E 180 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   SER E 182 " --> pdb=" O   PHE E 170 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 155 through 158

    962 hydrogen bonds defined for protein.
    2706 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.61

  Time building geometry restraints manager: 4.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4796
        1.34 -     1.46: 4029
        1.46 -     1.58: 7019
        1.58 -     1.70: 0
        1.70 -     1.82: 164
  Bond restraints: 16008
  Sorted by residual:
  bond pdb=" CG  PRO H 171 "
       pdb=" CD  PRO H 171 "
    ideal  model  delta    sigma   weight residual
    1.503  1.536 -0.033 3.40e-02 8.65e+02 9.44e-01
  bond pdb=" CG  PRO E 171 "
       pdb=" CD  PRO E 171 "
    ideal  model  delta    sigma   weight residual
    1.503  1.536 -0.033 3.40e-02 8.65e+02 9.32e-01
  bond pdb=" CA  ILE D1630 "
       pdb=" CB  ILE D1630 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 9.13e-01
  bond pdb=" CB  ARG E  38 "
       pdb=" CG  ARG E  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.40e-01
  bond pdb=" CB  ARG H  38 "
       pdb=" CG  ARG H  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.14e-01
  ... (remaining 16003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 20945
        1.21 -     2.41: 629
        2.41 -     3.62: 150
        3.62 -     4.83: 26
        4.83 -     6.03: 12
  Bond angle restraints: 21762
  Sorted by residual:
  angle pdb=" C   ILE L 205 "
        pdb=" N   VAL L 206 "
        pdb=" CA  VAL L 206 "
      ideal   model   delta    sigma   weight residual
     121.97  125.96   -3.99 1.80e+00 3.09e-01 4.92e+00
  angle pdb=" C   ILE F 205 "
        pdb=" N   VAL F 206 "
        pdb=" CA  VAL F 206 "
      ideal   model   delta    sigma   weight residual
     121.97  125.94   -3.97 1.80e+00 3.09e-01 4.86e+00
  angle pdb=" N   VAL H  48 "
        pdb=" CA  VAL H  48 "
        pdb=" C   VAL H  48 "
      ideal   model   delta    sigma   weight residual
     109.34  113.76   -4.42 2.08e+00 2.31e-01 4.51e+00
  angle pdb=" N   VAL E  48 "
        pdb=" CA  VAL E  48 "
        pdb=" C   VAL E  48 "
      ideal   model   delta    sigma   weight residual
     109.34  113.75   -4.41 2.08e+00 2.31e-01 4.49e+00
  angle pdb=" CA  CYS E  92 "
        pdb=" CB  CYS E  92 "
        pdb=" SG  CYS E  92 "
      ideal   model   delta    sigma   weight residual
     114.40  118.79   -4.39 2.30e+00 1.89e-01 3.65e+00
  ... (remaining 21757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 8695
       17.17 -    34.34: 578
       34.34 -    51.51: 121
       51.51 -    68.69: 25
       68.69 -    85.86: 35
  Dihedral angle restraints: 9454
    sinusoidal: 3706
      harmonic: 5748
  Sorted by residual:
  dihedral pdb=" CA  PRO E 123 "
           pdb=" C   PRO E 123 "
           pdb=" N   SER E 124 "
           pdb=" CA  SER E 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.06   23.94     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  PRO H 123 "
           pdb=" C   PRO H 123 "
           pdb=" N   SER H 124 "
           pdb=" CA  SER H 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.07   23.93     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  PRO H 153 "
           pdb=" C   PRO H 153 "
           pdb=" N   VAL H 154 "
           pdb=" CA  VAL H 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 9451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1458
       0.030 -    0.060: 737
       0.060 -    0.090: 226
       0.090 -    0.120: 104
       0.120 -    0.151: 5
  Chirality restraints: 2530
  Sorted by residual:
  chirality pdb=" CA  VAL E 173 "
            pdb=" N   VAL E 173 "
            pdb=" C   VAL E 173 "
            pdb=" CB  VAL E 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  VAL H 173 "
            pdb=" N   VAL H 173 "
            pdb=" C   VAL H 173 "
            pdb=" CB  VAL H 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.60e-01
  chirality pdb=" CA  ILE L 150 "
            pdb=" N   ILE L 150 "
            pdb=" C   ILE L 150 "
            pdb=" CB  ILE L 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 2527 not shown)

  Planarity restraints: 2678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 108 "   -0.366 9.50e-02 1.11e+02   1.65e-01 2.11e+01
        pdb=" NE  ARG L 108 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 108 "   -0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 108 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 108 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 108 "    0.364 9.50e-02 1.11e+02   1.64e-01 2.10e+01
        pdb=" NE  ARG F 108 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 108 "    0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 108 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 108 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  38 "   -0.217 9.50e-02 1.11e+02   9.80e-02 7.18e+00
        pdb=" NE  ARG H  38 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  38 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  38 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  38 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2675 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3041
        2.77 -     3.30: 16228
        3.30 -     3.84: 27016
        3.84 -     4.37: 32802
        4.37 -     4.90: 54123
  Nonbonded interactions: 133210
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 170 "
            pdb=" OG1 THR F 172 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OE1 GLU F 105 "
            pdb=" OH  TYR F 173 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD1 ASP L 151 "
            pdb=" OG  SER L 191 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OD1 ASP L 170 "
            pdb=" OG1 THR L 172 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OE1 GLU L 105 "
            pdb=" OH  TYR L 173 "
     model   vdw
     2.271 3.040
  ... (remaining 133205 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.040
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     34.840
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.060
  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:12.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
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      :  0.003   0.035  16008  Z= 0.184
  Angle     :  0.545   6.034  21762  Z= 0.285
  Chirality :  0.040   0.151   2530
  Planarity :  0.009   0.165   2678
  Dihedral  : 13.652  85.857   5708
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.20 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  4.37 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.18), residues: 1944
  helix: -0.88 (0.15), residues: 908
  sheet: -0.54 (0.26), residues: 388
  loop : -1.00 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 163 
 HIS   0.004   0.001   HIS C1742 
 PHE   0.018   0.001   PHE D1701 
 TYR   0.011   0.002   TYR E 102 
 ARG   0.037   0.004   ARG F 108 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 312
  time to evaluate  : 1.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1494 TYR cc_start: 0.7318 (t80) cc_final: 0.7062 (t80)
REVERT: A 1508 LYS cc_start: 0.8149 (mttm) cc_final: 0.7904 (mttm)
REVERT: A 1565 ASP cc_start: 0.8030 (t0) cc_final: 0.7700 (t0)
REVERT: A 1653 GLN cc_start: 0.8817 (tt0) cc_final: 0.8583 (mt0)
REVERT: A 1722 ASP cc_start: 0.8689 (t0) cc_final: 0.8468 (t0)
REVERT: A 1724 MET cc_start: 0.8577 (mmm) cc_final: 0.8215 (tpp)
REVERT: B 1571 ASP cc_start: 0.8723 (m-30) cc_final: 0.8312 (m-30)
REVERT: B 1614 THR cc_start: 0.9110 (m) cc_final: 0.8793 (p)
REVERT: B 1722 ASP cc_start: 0.8604 (t0) cc_final: 0.8256 (t0)
REVERT: B 1724 MET cc_start: 0.8399 (mmm) cc_final: 0.8101 (mmm)
REVERT: C 1508 LYS cc_start: 0.8109 (mttm) cc_final: 0.7872 (mttm)
REVERT: C 1565 ASP cc_start: 0.8029 (t0) cc_final: 0.7700 (t0)
REVERT: C 1653 GLN cc_start: 0.8867 (tt0) cc_final: 0.8620 (mt0)
REVERT: C 1722 ASP cc_start: 0.8754 (t0) cc_final: 0.8493 (t0)
REVERT: C 1724 MET cc_start: 0.8567 (mmm) cc_final: 0.8167 (tpp)
REVERT: D 1571 ASP cc_start: 0.8734 (m-30) cc_final: 0.8292 (m-30)
REVERT: D 1614 THR cc_start: 0.9120 (m) cc_final: 0.8800 (p)
REVERT: D 1722 ASP cc_start: 0.8582 (t0) cc_final: 0.8259 (t0)
REVERT: D 1724 MET cc_start: 0.8401 (mmm) cc_final: 0.8132 (mmm)
REVERT: H    3 GLN cc_start: 0.9159 (tt0) cc_final: 0.8872 (tp40)
REVERT: H   72 ASP cc_start: 0.8606 (t0) cc_final: 0.8033 (t0)
REVERT: H   75 LYS cc_start: 0.9225 (mttp) cc_final: 0.9000 (mtmt)
REVERT: L   53 LYS cc_start: 0.8640 (tttt) cc_final: 0.8388 (tttm)
REVERT: L   77 SER cc_start: 0.8398 (t) cc_final: 0.7967 (p)
REVERT: L   81 GLU cc_start: 0.8601 (pt0) cc_final: 0.8371 (pm20)
REVERT: L  185 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6192 (mm-30)
REVERT: F   17 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7493 (mt-10)
REVERT: F   53 LYS cc_start: 0.8648 (tttt) cc_final: 0.8411 (tttm)
REVERT: E    3 GLN cc_start: 0.9142 (tt0) cc_final: 0.8847 (tp40)
REVERT: E   72 ASP cc_start: 0.8580 (t0) cc_final: 0.8120 (t0)
REVERT: E   75 LYS cc_start: 0.9229 (mttp) cc_final: 0.9022 (mtmt)
  outliers start: 11
  outliers final: 2
  residues processed: 322
  average time/residue: 1.5092
  time to fit residues: 530.9582
Evaluate side-chains
  230 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 2.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain E residue  135 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 163 optimal weight:    7.9990
   chunk 147 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 152 optimal weight:    0.4980
   chunk 58 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 176 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** C1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  76 ASN
H 175 GLN
L 166 GLN
F 166 GLN
E  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.143447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.077480 restraints weight = 26603.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.59
r_work: 0.2806 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  16008  Z= 0.300
  Angle     :  0.642   8.331  21762  Z= 0.342
  Chirality :  0.044   0.171   2530
  Planarity :  0.005   0.040   2678
  Dihedral  :  5.449  51.479   2116
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.90 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.19), residues: 1944
  helix:  0.93 (0.17), residues: 882
  sheet: -0.43 (0.25), residues: 388
  loop : -0.28 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 103 
 HIS   0.006   0.001   HIS C1742 
 PHE   0.020   0.002   PHE E 150 
 TYR   0.019   0.002   TYR B1591 
 ARG   0.008   0.001   ARG C1496 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 262
  time to evaluate  : 1.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1494 TYR cc_start: 0.7620 (t80) cc_final: 0.7374 (t80)
REVERT: A 1524 GLU cc_start: 0.7455 (pp20) cc_final: 0.7242 (pp20)
REVERT: A 1582 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8102 (tmm)
REVERT: A 1653 GLN cc_start: 0.8842 (tt0) cc_final: 0.8467 (mt0)
REVERT: A 1722 ASP cc_start: 0.8487 (t0) cc_final: 0.8255 (t0)
REVERT: A 1724 MET cc_start: 0.8611 (mmm) cc_final: 0.8107 (tpp)
REVERT: B 1493 MET cc_start: 0.8264 (ptt) cc_final: 0.7984 (pp-130)
REVERT: B 1494 TYR cc_start: 0.7196 (t80) cc_final: 0.6995 (t80)
REVERT: B 1505 PHE cc_start: 0.8068 (t80) cc_final: 0.7799 (t80)
REVERT: B 1724 MET cc_start: 0.8503 (mmm) cc_final: 0.8206 (mmm)
REVERT: C 1524 GLU cc_start: 0.7462 (pp20) cc_final: 0.7247 (pp20)
REVERT: C 1582 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8021 (tmm)
REVERT: C 1653 GLN cc_start: 0.8859 (tt0) cc_final: 0.8470 (mt0)
REVERT: C 1722 ASP cc_start: 0.8494 (t0) cc_final: 0.8259 (t0)
REVERT: C 1724 MET cc_start: 0.8507 (mmm) cc_final: 0.8023 (tpp)
REVERT: D 1493 MET cc_start: 0.8257 (ptt) cc_final: 0.7993 (pp-130)
REVERT: D 1505 PHE cc_start: 0.8092 (t80) cc_final: 0.7820 (t80)
REVERT: D 1724 MET cc_start: 0.8464 (mmm) cc_final: 0.8203 (mmm)
REVERT: H    3 GLN cc_start: 0.9166 (tt0) cc_final: 0.8868 (tp40)
REVERT: H   72 ASP cc_start: 0.8548 (t0) cc_final: 0.8055 (t70)
REVERT: H   75 LYS cc_start: 0.9335 (mttp) cc_final: 0.9064 (mtmt)
REVERT: H  178 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: L   17 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: L   53 LYS cc_start: 0.8733 (tttt) cc_final: 0.8455 (tttm)
REVERT: L   81 GLU cc_start: 0.8918 (pt0) cc_final: 0.8688 (pm20)
REVERT: L  142 LYS cc_start: 0.8075 (tttp) cc_final: 0.7735 (mttt)
REVERT: F   53 LYS cc_start: 0.8739 (tttt) cc_final: 0.8465 (tttm)
REVERT: F  169 LYS cc_start: 0.8538 (pttt) cc_final: 0.8049 (pptt)
REVERT: E    3 GLN cc_start: 0.9156 (tt0) cc_final: 0.8855 (tp40)
REVERT: E   72 ASP cc_start: 0.8529 (t0) cc_final: 0.8030 (t70)
REVERT: E   75 LYS cc_start: 0.9338 (mttp) cc_final: 0.9062 (mtmt)
  outliers start: 26
  outliers final: 7
  residues processed: 276
  average time/residue: 1.4647
  time to fit residues: 442.8601
Evaluate side-chains
  245 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 235
  time to evaluate  : 2.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1548 THR
Chi-restraints excluded: chain A residue 1580 VAL
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain C residue 1548 THR
Chi-restraints excluded: chain C residue 1580 VAL
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue   41 GLU
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 162 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 155 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 141 optimal weight:    7.9990
   chunk 174 optimal weight:    0.6980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A1734 HIS
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1558 HIS
B1653 GLN
B1748 ASN
** C1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1734 HIS
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1540 ASN
D1558 HIS
D1653 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.142643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.076474 restraints weight = 26513.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.58
r_work: 0.2787 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  16008  Z= 0.362
  Angle     :  0.620   7.603  21762  Z= 0.327
  Chirality :  0.044   0.159   2530
  Planarity :  0.005   0.037   2678
  Dihedral  :  5.019  22.872   2112
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.66 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.19), residues: 1944
  helix:  1.29 (0.17), residues: 882
  sheet: -0.38 (0.25), residues: 388
  loop : -0.32 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP L 163 
 HIS   0.006   0.001   HIS B1742 
 PHE   0.022   0.002   PHE E 150 
 TYR   0.015   0.002   TYR L 140 
 ARG   0.004   0.001   ARG A1602 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 258
  time to evaluate  : 1.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1621 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8432 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8767 (tt0) cc_final: 0.8448 (mt0)
REVERT: A 1722 ASP cc_start: 0.8484 (t0) cc_final: 0.8270 (t0)
REVERT: A 1724 MET cc_start: 0.8598 (mmm) cc_final: 0.8122 (tpp)
REVERT: B 1505 PHE cc_start: 0.8081 (t80) cc_final: 0.7842 (t80)
REVERT: B 1507 THR cc_start: 0.8461 (m) cc_final: 0.8170 (p)
REVERT: B 1530 GLN cc_start: 0.8832 (tp40) cc_final: 0.8540 (tm-30)
REVERT: B 1571 ASP cc_start: 0.8469 (m-30) cc_final: 0.8224 (t0)
REVERT: B 1619 MET cc_start: 0.9450 (mmm) cc_final: 0.9250 (mmp)
REVERT: B 1724 MET cc_start: 0.8541 (mmm) cc_final: 0.8278 (mmm)
REVERT: C 1493 MET cc_start: 0.8146 (mmp) cc_final: 0.7653 (ttt)
REVERT: C 1559 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7536 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8065 (tmm)
REVERT: C 1621 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8414 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8774 (tt0) cc_final: 0.8467 (mt0)
REVERT: C 1722 ASP cc_start: 0.8518 (t0) cc_final: 0.8306 (t0)
REVERT: C 1724 MET cc_start: 0.8578 (mmm) cc_final: 0.8079 (tpp)
REVERT: D 1494 TYR cc_start: 0.7007 (t80) cc_final: 0.6510 (t80)
REVERT: D 1505 PHE cc_start: 0.8118 (t80) cc_final: 0.7869 (t80)
REVERT: D 1507 THR cc_start: 0.8456 (m) cc_final: 0.8166 (p)
REVERT: D 1530 GLN cc_start: 0.8819 (tp40) cc_final: 0.8533 (tm-30)
REVERT: D 1571 ASP cc_start: 0.8482 (m-30) cc_final: 0.8256 (t0)
REVERT: D 1582 MET cc_start: 0.8329 (ttm) cc_final: 0.8124 (ttt)
REVERT: D 1619 MET cc_start: 0.9452 (mmm) cc_final: 0.9249 (mmp)
REVERT: D 1724 MET cc_start: 0.8500 (mmm) cc_final: 0.8260 (mmm)
REVERT: H    3 GLN cc_start: 0.9244 (tt0) cc_final: 0.8952 (tp40)
REVERT: H   72 ASP cc_start: 0.8679 (t0) cc_final: 0.7900 (t70)
REVERT: H   75 LYS cc_start: 0.9306 (mttp) cc_final: 0.8995 (mtmt)
REVERT: H  178 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8906 (mt)
REVERT: L   53 LYS cc_start: 0.8696 (tttt) cc_final: 0.8441 (tttm)
REVERT: L   81 GLU cc_start: 0.8919 (pt0) cc_final: 0.8639 (pm20)
REVERT: L  169 LYS cc_start: 0.8584 (pttt) cc_final: 0.8250 (pptt)
REVERT: L  175 MET cc_start: 0.5538 (ttt) cc_final: 0.5320 (ttt)
REVERT: F   53 LYS cc_start: 0.8717 (tttt) cc_final: 0.8467 (tttm)
REVERT: F  175 MET cc_start: 0.6024 (ttt) cc_final: 0.5801 (ttt)
REVERT: F  195 GLU cc_start: 0.5647 (mt-10) cc_final: 0.5114 (mm-30)
REVERT: E    3 GLN cc_start: 0.9237 (tt0) cc_final: 0.8942 (tp40)
REVERT: E   72 ASP cc_start: 0.8651 (t0) cc_final: 0.7851 (t70)
REVERT: E   75 LYS cc_start: 0.9315 (mttp) cc_final: 0.8991 (mtmt)
REVERT: E  177 ASP cc_start: 0.8906 (m-30) cc_final: 0.8530 (m-30)
  outliers start: 38
  outliers final: 10
  residues processed: 277
  average time/residue: 1.4452
  time to fit residues: 438.4990
Evaluate side-chains
  251 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 239
  time to evaluate  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1548 THR
Chi-restraints excluded: chain A residue 1577 ILE
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain C residue 1548 THR
Chi-restraints excluded: chain C residue 1577 ILE
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 137 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 188 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9980
   chunk 123 optimal weight:    0.0770
   chunk 108 optimal weight:    0.9990
   chunk 153 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 181 optimal weight:    0.8980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1531 HIS
B1653 GLN
** C1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1531 HIS
D1653 GLN
F 138 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.144475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.079259 restraints weight = 26364.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.58
r_work: 0.2841 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16008  Z= 0.196
  Angle     :  0.573   7.995  21762  Z= 0.297
  Chirality :  0.042   0.149   2530
  Planarity :  0.004   0.048   2678
  Dihedral  :  4.721  25.146   2112
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.28 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.19), residues: 1944
  helix:  1.52 (0.17), residues: 906
  sheet: -0.25 (0.25), residues: 392
  loop : -0.55 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP L 163 
 HIS   0.004   0.001   HIS B1742 
 PHE   0.013   0.001   PHE E 150 
 TYR   0.014   0.001   TYR F 140 
 ARG   0.003   0.000   ARG A1496 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 258
  time to evaluate  : 1.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8392 (tpp) cc_final: 0.7914 (ttt)
REVERT: A 1559 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7519 (mtt-85)
REVERT: A 1582 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7767 (tmt)
REVERT: A 1621 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8400 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8727 (tt0) cc_final: 0.8393 (mt0)
REVERT: B 1494 TYR cc_start: 0.6984 (t80) cc_final: 0.6472 (t80)
REVERT: B 1505 PHE cc_start: 0.7949 (t80) cc_final: 0.7724 (t80)
REVERT: B 1507 THR cc_start: 0.8384 (m) cc_final: 0.8112 (p)
REVERT: B 1530 GLN cc_start: 0.8819 (tp40) cc_final: 0.8463 (tm-30)
REVERT: B 1571 ASP cc_start: 0.8455 (m-30) cc_final: 0.8246 (t0)
REVERT: B 1619 MET cc_start: 0.9403 (mmm) cc_final: 0.9197 (mmp)
REVERT: B 1724 MET cc_start: 0.8525 (mmm) cc_final: 0.8261 (mmm)
REVERT: C 1559 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7459 (mtt-85)
REVERT: C 1621 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8373 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8721 (tt0) cc_final: 0.8396 (mt0)
REVERT: C 1724 MET cc_start: 0.8586 (mmm) cc_final: 0.8354 (mmm)
REVERT: D 1494 TYR cc_start: 0.7052 (t80) cc_final: 0.6531 (t80)
REVERT: D 1505 PHE cc_start: 0.7940 (t80) cc_final: 0.7716 (t80)
REVERT: D 1507 THR cc_start: 0.8384 (m) cc_final: 0.8120 (p)
REVERT: D 1530 GLN cc_start: 0.8815 (tp40) cc_final: 0.8467 (tm-30)
REVERT: D 1619 MET cc_start: 0.9409 (mmm) cc_final: 0.9205 (mmp)
REVERT: D 1724 MET cc_start: 0.8504 (mmm) cc_final: 0.8259 (mmm)
REVERT: H    3 GLN cc_start: 0.9224 (tt0) cc_final: 0.8949 (tp40)
REVERT: H   72 ASP cc_start: 0.8665 (t0) cc_final: 0.7809 (t70)
REVERT: H   75 LYS cc_start: 0.9327 (mttp) cc_final: 0.9004 (mtmt)
REVERT: H  147 LYS cc_start: 0.6533 (mtpp) cc_final: 0.6036 (tttt)
REVERT: H  178 LEU cc_start: 0.9200 (mp) cc_final: 0.8923 (mt)
REVERT: L   53 LYS cc_start: 0.8682 (tttt) cc_final: 0.8411 (tttm)
REVERT: L   81 GLU cc_start: 0.8935 (pt0) cc_final: 0.8671 (pm20)
REVERT: L  169 LYS cc_start: 0.8651 (pttt) cc_final: 0.8332 (pttm)
REVERT: L  175 MET cc_start: 0.5605 (ttt) cc_final: 0.5009 (ttt)
REVERT: F   53 LYS cc_start: 0.8707 (tttt) cc_final: 0.8441 (tttm)
REVERT: F   78 MET cc_start: 0.8589 (ttt) cc_final: 0.8272 (ttm)
REVERT: F  169 LYS cc_start: 0.8679 (pttt) cc_final: 0.8340 (pptt)
REVERT: F  175 MET cc_start: 0.5981 (ttt) cc_final: 0.5712 (ttt)
REVERT: F  195 GLU cc_start: 0.5990 (mt-10) cc_final: 0.5426 (mm-30)
REVERT: E    3 GLN cc_start: 0.9173 (tt0) cc_final: 0.8894 (tp40)
REVERT: E   72 ASP cc_start: 0.8641 (t0) cc_final: 0.7763 (t70)
REVERT: E   75 LYS cc_start: 0.9323 (mttp) cc_final: 0.8995 (mtmt)
REVERT: E   85 GLU cc_start: 0.8927 (mp0) cc_final: 0.8529 (mp0)
  outliers start: 33
  outliers final: 6
  residues processed: 273
  average time/residue: 1.4245
  time to fit residues: 427.9686
Evaluate side-chains
  247 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 240
  time to evaluate  : 1.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1577 ILE
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain C residue 1577 ILE
Chi-restraints excluded: chain C residue 1691 MET
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain F residue  172 THR
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 168 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 179 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 180 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 126 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A1517 ASN
A1540 ASN
** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** B1748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1517 ASN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 GLN
H 200 ASN
E 200 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.141616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.075836 restraints weight = 26714.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.54
r_work: 0.2775 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2659 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  16008  Z= 0.460
  Angle     :  0.650   8.481  21762  Z= 0.337
  Chirality :  0.045   0.165   2530
  Planarity :  0.005   0.051   2678
  Dihedral  :  4.825  23.624   2112
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.70 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.19), residues: 1944
  helix:  1.39 (0.17), residues: 908
  sheet: -0.31 (0.26), residues: 396
  loop : -0.52 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 103 
 HIS   0.003   0.001   HIS D1742 
 PHE   0.023   0.002   PHE H 150 
 TYR   0.029   0.002   TYR F 140 
 ARG   0.010   0.001   ARG F 108 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 242
  time to evaluate  : 1.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8453 (tpp) cc_final: 0.8009 (ttt)
REVERT: A 1582 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (tmm)
REVERT: A 1621 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8453 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8765 (tt0) cc_final: 0.8401 (mt0)
REVERT: A 1724 MET cc_start: 0.8529 (mmm) cc_final: 0.7949 (tpp)
REVERT: B 1505 PHE cc_start: 0.8034 (t80) cc_final: 0.7820 (t80)
REVERT: B 1507 THR cc_start: 0.8490 (m) cc_final: 0.8187 (p)
REVERT: B 1530 GLN cc_start: 0.8858 (tp40) cc_final: 0.8497 (tm-30)
REVERT: B 1571 ASP cc_start: 0.8478 (m-30) cc_final: 0.8232 (t0)
REVERT: B 1619 MET cc_start: 0.9475 (mmm) cc_final: 0.9272 (mmp)
REVERT: B 1722 ASP cc_start: 0.8479 (t0) cc_final: 0.8267 (t70)
REVERT: B 1724 MET cc_start: 0.8567 (mmm) cc_final: 0.8240 (mmm)
REVERT: C 1493 MET cc_start: 0.8363 (tpp) cc_final: 0.7948 (ttt)
REVERT: C 1537 TYR cc_start: 0.7511 (t80) cc_final: 0.7279 (t80)
REVERT: C 1582 MET cc_start: 0.8170 (tmm) cc_final: 0.7794 (tmm)
REVERT: C 1621 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8440 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8795 (tt0) cc_final: 0.8433 (mt0)
REVERT: C 1724 MET cc_start: 0.8608 (mmm) cc_final: 0.8082 (tpp)
REVERT: D 1494 TYR cc_start: 0.7020 (t80) cc_final: 0.6510 (t80)
REVERT: D 1505 PHE cc_start: 0.8065 (t80) cc_final: 0.7843 (t80)
REVERT: D 1507 THR cc_start: 0.8494 (m) cc_final: 0.8192 (p)
REVERT: D 1530 GLN cc_start: 0.8845 (tp40) cc_final: 0.8491 (tm-30)
REVERT: D 1540 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7408 (t0)
REVERT: D 1619 MET cc_start: 0.9481 (mmm) cc_final: 0.9277 (mmp)
REVERT: D 1722 ASP cc_start: 0.8477 (t0) cc_final: 0.8244 (t70)
REVERT: D 1724 MET cc_start: 0.8541 (mmm) cc_final: 0.8236 (mmm)
REVERT: H    3 GLN cc_start: 0.9280 (tt0) cc_final: 0.8984 (tp40)
REVERT: H   72 ASP cc_start: 0.8718 (t0) cc_final: 0.7835 (t70)
REVERT: H   75 LYS cc_start: 0.9324 (mttp) cc_final: 0.8996 (mtmt)
REVERT: H  147 LYS cc_start: 0.6669 (mtpp) cc_final: 0.6202 (tttt)
REVERT: L   53 LYS cc_start: 0.8677 (tttt) cc_final: 0.8427 (tttm)
REVERT: L   81 GLU cc_start: 0.8920 (pt0) cc_final: 0.8639 (pm20)
REVERT: L  169 LYS cc_start: 0.8605 (pttt) cc_final: 0.8232 (pptt)
REVERT: L  175 MET cc_start: 0.5587 (ttt) cc_final: 0.5044 (ttt)
REVERT: F   53 LYS cc_start: 0.8695 (tttt) cc_final: 0.8455 (tttm)
REVERT: F   78 MET cc_start: 0.8568 (ttt) cc_final: 0.8248 (ttm)
REVERT: F  175 MET cc_start: 0.5912 (ttt) cc_final: 0.5268 (ttt)
REVERT: E    3 GLN cc_start: 0.9253 (tt0) cc_final: 0.8975 (tp40)
REVERT: E   72 ASP cc_start: 0.8693 (t0) cc_final: 0.7786 (t70)
REVERT: E   75 LYS cc_start: 0.9315 (mttp) cc_final: 0.8981 (mtmt)
REVERT: E  177 ASP cc_start: 0.8991 (m-30) cc_final: 0.8583 (m-30)
  outliers start: 44
  outliers final: 18
  residues processed: 267
  average time/residue: 1.4877
  time to fit residues: 436.3999
Evaluate side-chains
  252 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1548 THR
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1577 ILE
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1548 THR
Chi-restraints excluded: chain C residue 1557 VAL
Chi-restraints excluded: chain C residue 1577 ILE
Chi-restraints excluded: chain D residue 1540 ASN
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  200 ASN
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue   10 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain E residue  200 ASN
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 176 optimal weight:    0.5980
   chunk 123 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 156 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 164 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 166 optimal weight:    4.9990
   chunk 152 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1540 ASN
D1653 GLN
H 200 ASN
E 159 ASN
E 200 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.143701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.078074 restraints weight = 26515.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.58
r_work: 0.2822 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16008  Z= 0.216
  Angle     :  0.586   9.123  21762  Z= 0.301
  Chirality :  0.042   0.155   2530
  Planarity :  0.004   0.054   2678
  Dihedral  :  4.618  24.164   2112
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.63 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.19), residues: 1944
  helix:  1.52 (0.17), residues: 936
  sheet: -0.22 (0.26), residues: 392
  loop : -0.55 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP L 163 
 HIS   0.004   0.001   HIS F  94 
 PHE   0.015   0.001   PHE H 150 
 TYR   0.030   0.001   TYR F 140 
 ARG   0.006   0.000   ARG F 108 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 249
  time to evaluate  : 1.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8514 (tpp) cc_final: 0.8074 (ttt)
REVERT: A 1559 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7500 (mtt-85)
REVERT: A 1621 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8393 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8700 (tt0) cc_final: 0.8352 (mt0)
REVERT: A 1724 MET cc_start: 0.8516 (mmm) cc_final: 0.7987 (tpp)
REVERT: B 1505 PHE cc_start: 0.7906 (t80) cc_final: 0.7696 (t80)
REVERT: B 1507 THR cc_start: 0.8414 (m) cc_final: 0.8149 (p)
REVERT: B 1571 ASP cc_start: 0.8478 (m-30) cc_final: 0.8207 (t0)
REVERT: B 1619 MET cc_start: 0.9440 (mmm) cc_final: 0.9224 (mmp)
REVERT: B 1722 ASP cc_start: 0.8442 (t0) cc_final: 0.8230 (t70)
REVERT: B 1724 MET cc_start: 0.8508 (mmm) cc_final: 0.8252 (mmm)
REVERT: C 1493 MET cc_start: 0.8452 (tpp) cc_final: 0.8004 (ttt)
REVERT: C 1559 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7529 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7774 (tmm)
REVERT: C 1621 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8383 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8716 (tt0) cc_final: 0.8354 (mt0)
REVERT: D 1494 TYR cc_start: 0.7095 (t80) cc_final: 0.6636 (t80)
REVERT: D 1505 PHE cc_start: 0.7916 (t80) cc_final: 0.7708 (t80)
REVERT: D 1507 THR cc_start: 0.8392 (m) cc_final: 0.8142 (p)
REVERT: D 1530 GLN cc_start: 0.8870 (tp40) cc_final: 0.8512 (tm-30)
REVERT: D 1619 MET cc_start: 0.9434 (mmm) cc_final: 0.9217 (mmp)
REVERT: D 1722 ASP cc_start: 0.8426 (t0) cc_final: 0.8183 (t70)
REVERT: D 1724 MET cc_start: 0.8510 (mmm) cc_final: 0.8165 (mmm)
REVERT: H    3 GLN cc_start: 0.9263 (tt0) cc_final: 0.9003 (tp40)
REVERT: H   72 ASP cc_start: 0.8661 (t0) cc_final: 0.7814 (t70)
REVERT: H   75 LYS cc_start: 0.9312 (mttp) cc_final: 0.8997 (mtmt)
REVERT: H  147 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6292 (tttt)
REVERT: L   53 LYS cc_start: 0.8693 (tttt) cc_final: 0.8451 (tttm)
REVERT: L   81 GLU cc_start: 0.8938 (pt0) cc_final: 0.8685 (pm20)
REVERT: L  169 LYS cc_start: 0.8603 (pttt) cc_final: 0.8329 (pptt)
REVERT: L  175 MET cc_start: 0.5685 (ttt) cc_final: 0.5162 (ttt)
REVERT: F   53 LYS cc_start: 0.8703 (tttt) cc_final: 0.8465 (tttm)
REVERT: F   78 MET cc_start: 0.8585 (ttt) cc_final: 0.8288 (ttm)
REVERT: F  175 MET cc_start: 0.5996 (ttt) cc_final: 0.5372 (ttt)
REVERT: F  195 GLU cc_start: 0.5917 (mt-10) cc_final: 0.5513 (mm-30)
REVERT: E    3 GLN cc_start: 0.9255 (tt0) cc_final: 0.8994 (tp40)
REVERT: E   72 ASP cc_start: 0.8654 (t0) cc_final: 0.7671 (t70)
REVERT: E   75 LYS cc_start: 0.9304 (mttp) cc_final: 0.8972 (mtmt)
REVERT: E  177 ASP cc_start: 0.8929 (m-30) cc_final: 0.8497 (m-30)
  outliers start: 27
  outliers final: 14
  residues processed: 261
  average time/residue: 1.6197
  time to fit residues: 460.4233
Evaluate side-chains
  250 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 235
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1577 ILE
Chi-restraints excluded: chain A residue 1633 MET
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain C residue 1633 MET
Chi-restraints excluded: chain D residue 1499 ASN
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain F residue   40 SER
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 165 optimal weight:    5.9990
   chunk 171 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 162 optimal weight:    0.9990
   chunk 187 optimal weight:    0.9980
   chunk 193 optimal weight:    7.9990
   chunk 142 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 GLN
L 156 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.143758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.078261 restraints weight = 26325.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.58
r_work: 0.2805 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16008  Z= 0.238
  Angle     :  0.592   9.406  21762  Z= 0.304
  Chirality :  0.042   0.158   2530
  Planarity :  0.004   0.055   2678
  Dihedral  :  4.528  23.592   2112
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.03 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.19), residues: 1944
  helix:  1.60 (0.17), residues: 936
  sheet: -0.17 (0.26), residues: 396
  loop : -0.48 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP L 163 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.015   0.001   PHE H 150 
 TYR   0.025   0.001   TYR F 140 
 ARG   0.009   0.000   ARG F 108 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 242
  time to evaluate  : 1.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8520 (tpp) cc_final: 0.8089 (ttt)
REVERT: A 1559 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7507 (mtt-85)
REVERT: A 1621 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8391 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8679 (tt0) cc_final: 0.8317 (mt0)
REVERT: A 1724 MET cc_start: 0.8559 (mmm) cc_final: 0.8324 (mmm)
REVERT: B 1507 THR cc_start: 0.8372 (m) cc_final: 0.8124 (p)
REVERT: B 1619 MET cc_start: 0.9408 (mmm) cc_final: 0.9179 (mmp)
REVERT: B 1722 ASP cc_start: 0.8449 (t0) cc_final: 0.8242 (t70)
REVERT: B 1724 MET cc_start: 0.8439 (mmm) cc_final: 0.8187 (mmm)
REVERT: C 1493 MET cc_start: 0.8466 (tpp) cc_final: 0.8034 (ttt)
REVERT: C 1559 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7502 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7591 (tmm)
REVERT: C 1621 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8380 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8661 (tt0) cc_final: 0.8359 (mt0)
REVERT: C 1724 MET cc_start: 0.8460 (mmm) cc_final: 0.7858 (tpp)
REVERT: D 1505 PHE cc_start: 0.7926 (t80) cc_final: 0.7725 (t80)
REVERT: D 1507 THR cc_start: 0.8368 (m) cc_final: 0.8132 (p)
REVERT: D 1619 MET cc_start: 0.9411 (mmm) cc_final: 0.9182 (mmp)
REVERT: D 1722 ASP cc_start: 0.8456 (t0) cc_final: 0.8229 (t70)
REVERT: D 1724 MET cc_start: 0.8456 (mmm) cc_final: 0.8160 (mmm)
REVERT: H    3 GLN cc_start: 0.9263 (tt0) cc_final: 0.8995 (tp40)
REVERT: H   72 ASP cc_start: 0.8655 (t0) cc_final: 0.7871 (t70)
REVERT: H   75 LYS cc_start: 0.9309 (mttp) cc_final: 0.8988 (mtmt)
REVERT: L   53 LYS cc_start: 0.8643 (tttt) cc_final: 0.8401 (tttm)
REVERT: L   81 GLU cc_start: 0.8907 (pt0) cc_final: 0.8630 (pm20)
REVERT: L  169 LYS cc_start: 0.8605 (pttt) cc_final: 0.8371 (pptt)
REVERT: L  175 MET cc_start: 0.5534 (ttt) cc_final: 0.5059 (ttt)
REVERT: L  210 ASN cc_start: 0.8457 (t0) cc_final: 0.7400 (t0)
REVERT: L  211 ARG cc_start: 0.6536 (ptm160) cc_final: 0.6115 (ptm160)
REVERT: F   53 LYS cc_start: 0.8636 (tttt) cc_final: 0.8395 (tttm)
REVERT: F   78 MET cc_start: 0.8540 (ttt) cc_final: 0.8163 (ttm)
REVERT: F  175 MET cc_start: 0.5873 (ttt) cc_final: 0.5290 (ttt)
REVERT: E    3 GLN cc_start: 0.9259 (tt0) cc_final: 0.8987 (tp40)
REVERT: E   72 ASP cc_start: 0.8635 (t0) cc_final: 0.7723 (t70)
REVERT: E   75 LYS cc_start: 0.9313 (mttp) cc_final: 0.8974 (mtmt)
REVERT: E  177 ASP cc_start: 0.8909 (m-30) cc_final: 0.8491 (m-30)
  outliers start: 29
  outliers final: 12
  residues processed: 252
  average time/residue: 1.4718
  time to fit residues: 405.5709
Evaluate side-chains
  246 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 233
  time to evaluate  : 1.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain D residue 1691 MET
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  169 LYS
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 44 optimal weight:    0.3980
   chunk 109 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9990
   chunk 154 optimal weight:    0.9990
   chunk 160 optimal weight:    0.7980
   chunk 138 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 150 optimal weight:    0.7980
   chunk 79 optimal weight:    9.9990
   chunk 188 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.144422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.079156 restraints weight = 26102.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.56
r_work: 0.2822 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16008  Z= 0.206
  Angle     :  0.596   8.886  21762  Z= 0.303
  Chirality :  0.041   0.160   2530
  Planarity :  0.004   0.057   2678
  Dihedral  :  4.444  22.883   2112
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 17.82 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.19), residues: 1944
  helix:  1.68 (0.17), residues: 936
  sheet: -0.09 (0.26), residues: 396
  loop : -0.44 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 163 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.023   0.001   PHE B1505 
 TYR   0.021   0.001   TYR F 140 
 ARG   0.008   0.000   ARG H  55 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 239
  time to evaluate  : 1.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8522 (tpp) cc_final: 0.8097 (ttt)
REVERT: A 1559 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7497 (mtt-85)
REVERT: A 1621 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8341 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8665 (tt0) cc_final: 0.8299 (mt0)
REVERT: A 1724 MET cc_start: 0.8552 (mmm) cc_final: 0.7928 (tpp)
REVERT: B 1507 THR cc_start: 0.8346 (m) cc_final: 0.8118 (p)
REVERT: B 1619 MET cc_start: 0.9393 (mmm) cc_final: 0.9192 (mmp)
REVERT: B 1722 ASP cc_start: 0.8411 (t0) cc_final: 0.8191 (t70)
REVERT: B 1724 MET cc_start: 0.8434 (mmm) cc_final: 0.8192 (mmm)
REVERT: C 1493 MET cc_start: 0.8472 (tpp) cc_final: 0.8039 (ttt)
REVERT: C 1559 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7484 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7632 (tmm)
REVERT: C 1621 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8333 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8650 (tt0) cc_final: 0.8320 (mt0)
REVERT: C 1724 MET cc_start: 0.8466 (mmm) cc_final: 0.7853 (tpp)
REVERT: D 1507 THR cc_start: 0.8365 (m) cc_final: 0.8131 (p)
REVERT: D 1619 MET cc_start: 0.9378 (mmm) cc_final: 0.9178 (mmp)
REVERT: D 1722 ASP cc_start: 0.8444 (t0) cc_final: 0.8217 (t70)
REVERT: D 1724 MET cc_start: 0.8439 (mmm) cc_final: 0.8218 (mmm)
REVERT: H    3 GLN cc_start: 0.9257 (tt0) cc_final: 0.8996 (tp40)
REVERT: H   72 ASP cc_start: 0.8652 (t0) cc_final: 0.7803 (t70)
REVERT: H   75 LYS cc_start: 0.9308 (mttp) cc_final: 0.8993 (mtmt)
REVERT: H  147 LYS cc_start: 0.6523 (mtpp) cc_final: 0.6078 (tttt)
REVERT: L   53 LYS cc_start: 0.8640 (tttt) cc_final: 0.8405 (tttm)
REVERT: L   81 GLU cc_start: 0.8942 (pt0) cc_final: 0.8642 (pm20)
REVERT: L  175 MET cc_start: 0.5589 (ttt) cc_final: 0.5118 (ttt)
REVERT: F   53 LYS cc_start: 0.8649 (tttt) cc_final: 0.8414 (tttm)
REVERT: F   78 MET cc_start: 0.8515 (ttt) cc_final: 0.8192 (ttm)
REVERT: F  169 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8377 (pptt)
REVERT: E    3 GLN cc_start: 0.9247 (tt0) cc_final: 0.8993 (tp40)
REVERT: E   72 ASP cc_start: 0.8627 (t0) cc_final: 0.7742 (t70)
REVERT: E   75 LYS cc_start: 0.9306 (mttp) cc_final: 0.8990 (mtmt)
  outliers start: 18
  outliers final: 13
  residues processed: 248
  average time/residue: 1.4320
  time to fit residues: 389.3396
Evaluate side-chains
  248 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 233
  time to evaluate  : 1.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain C residue 1691 MET
Chi-restraints excluded: chain D residue 1582 MET
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain D residue 1691 MET
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  169 LYS
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 187 optimal weight:    0.7980
   chunk 160 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   chunk 158 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   chunk 179 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.144127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.079205 restraints weight = 26539.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.55
r_work: 0.2837 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16008  Z= 0.233
  Angle     :  0.615   9.356  21762  Z= 0.310
  Chirality :  0.042   0.163   2530
  Planarity :  0.004   0.058   2678
  Dihedral  :  4.412  22.491   2112
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.99 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.19), residues: 1944
  helix:  1.65 (0.17), residues: 940
  sheet: -0.04 (0.27), residues: 396
  loop : -0.42 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP F 163 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.014   0.001   PHE H 150 
 TYR   0.022   0.001   TYR C1537 
 ARG   0.008   0.000   ARG F 108 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 236
  time to evaluate  : 1.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8523 (tpp) cc_final: 0.8111 (ttt)
REVERT: A 1559 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7508 (mtt-85)
REVERT: A 1621 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8367 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8664 (tt0) cc_final: 0.8301 (mt0)
REVERT: A 1724 MET cc_start: 0.8624 (mmm) cc_final: 0.8400 (mmm)
REVERT: B 1507 THR cc_start: 0.8389 (m) cc_final: 0.8149 (p)
REVERT: B 1619 MET cc_start: 0.9411 (mmm) cc_final: 0.9186 (mmp)
REVERT: B 1722 ASP cc_start: 0.8461 (t0) cc_final: 0.8248 (t70)
REVERT: B 1724 MET cc_start: 0.8507 (mmm) cc_final: 0.8249 (mmm)
REVERT: C 1493 MET cc_start: 0.8472 (tpp) cc_final: 0.8030 (ttt)
REVERT: C 1559 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7466 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7651 (tmm)
REVERT: C 1621 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8372 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8659 (tt0) cc_final: 0.8318 (mt0)
REVERT: C 1724 MET cc_start: 0.8520 (mmm) cc_final: 0.7915 (tpp)
REVERT: D 1507 THR cc_start: 0.8375 (m) cc_final: 0.8144 (p)
REVERT: D 1619 MET cc_start: 0.9399 (mmm) cc_final: 0.9169 (mmp)
REVERT: D 1722 ASP cc_start: 0.8490 (t0) cc_final: 0.8269 (t70)
REVERT: D 1724 MET cc_start: 0.8514 (mmm) cc_final: 0.8203 (mmm)
REVERT: H    3 GLN cc_start: 0.9273 (tt0) cc_final: 0.9013 (tp40)
REVERT: H   72 ASP cc_start: 0.8680 (t0) cc_final: 0.7834 (t70)
REVERT: H   75 LYS cc_start: 0.9326 (mttp) cc_final: 0.9010 (mtmt)
REVERT: H  147 LYS cc_start: 0.6617 (mtpp) cc_final: 0.6185 (tttt)
REVERT: L   53 LYS cc_start: 0.8668 (tttt) cc_final: 0.8440 (tttm)
REVERT: L   81 GLU cc_start: 0.8945 (pt0) cc_final: 0.8662 (pm20)
REVERT: F   53 LYS cc_start: 0.8668 (tttt) cc_final: 0.8442 (tttm)
REVERT: F  169 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8375 (pptt)
REVERT: E    3 GLN cc_start: 0.9268 (tt0) cc_final: 0.9014 (tp40)
REVERT: E   72 ASP cc_start: 0.8647 (t0) cc_final: 0.7742 (t70)
REVERT: E   75 LYS cc_start: 0.9324 (mttp) cc_final: 0.9001 (mtmt)
  outliers start: 22
  outliers final: 14
  residues processed: 244
  average time/residue: 1.4528
  time to fit residues: 387.7881
Evaluate side-chains
  245 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 229
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1532 MET
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain D residue 1582 MET
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain D residue 1691 MET
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  169 LYS
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 183 optimal weight:    0.6980
   chunk 193 optimal weight:    7.9990
   chunk 34 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 64 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 156 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.144339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.079157 restraints weight = 26358.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.57
r_work: 0.2822 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16008  Z= 0.223
  Angle     :  0.618   9.230  21762  Z= 0.313
  Chirality :  0.041   0.168   2530
  Planarity :  0.004   0.058   2678
  Dihedral  :  4.376  22.967   2112
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.56 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.19), residues: 1944
  helix:  1.69 (0.17), residues: 940
  sheet:  0.02 (0.27), residues: 396
  loop : -0.39 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP F 163 
 HIS   0.003   0.001   HIS F  94 
 PHE   0.024   0.001   PHE B1505 
 TYR   0.021   0.001   TYR F 140 
 ARG   0.008   0.000   ARG H  55 

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

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

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3888 Ramachandran restraints generated.
    1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 235
  time to evaluate  : 1.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1493 MET cc_start: 0.8539 (tpp) cc_final: 0.8132 (ttt)
REVERT: A 1559 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7445 (mtt-85)
REVERT: A 1621 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8373 (ttmm)
REVERT: A 1653 GLN cc_start: 0.8652 (tt0) cc_final: 0.8288 (mt0)
REVERT: A 1724 MET cc_start: 0.8526 (mmm) cc_final: 0.7920 (tpp)
REVERT: B 1507 THR cc_start: 0.8345 (m) cc_final: 0.8110 (p)
REVERT: B 1619 MET cc_start: 0.9392 (mmm) cc_final: 0.9161 (mmp)
REVERT: B 1722 ASP cc_start: 0.8424 (t0) cc_final: 0.8214 (t70)
REVERT: B 1724 MET cc_start: 0.8466 (mmm) cc_final: 0.8231 (mmm)
REVERT: C 1493 MET cc_start: 0.8472 (tpp) cc_final: 0.8032 (ttt)
REVERT: C 1559 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7435 (mtt-85)
REVERT: C 1582 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7644 (tmm)
REVERT: C 1621 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8360 (ttmm)
REVERT: C 1653 GLN cc_start: 0.8637 (tt0) cc_final: 0.8305 (mt0)
REVERT: C 1724 MET cc_start: 0.8476 (mmm) cc_final: 0.7892 (tpp)
REVERT: D 1507 THR cc_start: 0.8343 (m) cc_final: 0.8122 (p)
REVERT: D 1619 MET cc_start: 0.9384 (mmm) cc_final: 0.9157 (mmp)
REVERT: D 1722 ASP cc_start: 0.8405 (t0) cc_final: 0.8165 (t70)
REVERT: D 1724 MET cc_start: 0.8479 (mmm) cc_final: 0.8156 (mmm)
REVERT: H    3 GLN cc_start: 0.9264 (tt0) cc_final: 0.9006 (tp40)
REVERT: H   72 ASP cc_start: 0.8672 (t0) cc_final: 0.7855 (t70)
REVERT: H   75 LYS cc_start: 0.9318 (mttp) cc_final: 0.8982 (mtmt)
REVERT: H  147 LYS cc_start: 0.6478 (mtpp) cc_final: 0.6047 (tttt)
REVERT: L   53 LYS cc_start: 0.8619 (tttt) cc_final: 0.8395 (tttm)
REVERT: L   81 GLU cc_start: 0.8906 (pt0) cc_final: 0.8652 (pm20)
REVERT: F   53 LYS cc_start: 0.8619 (tttt) cc_final: 0.8394 (tttm)
REVERT: F   78 MET cc_start: 0.8476 (ttt) cc_final: 0.8235 (ttm)
REVERT: F  169 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (pptt)
REVERT: F  211 ARG cc_start: 0.5639 (ttp80) cc_final: 0.5405 (ttp80)
REVERT: E    3 GLN cc_start: 0.9246 (tt0) cc_final: 0.8989 (tp40)
REVERT: E   72 ASP cc_start: 0.8634 (t0) cc_final: 0.7759 (t70)
REVERT: E   75 LYS cc_start: 0.9325 (mttp) cc_final: 0.8994 (mtmt)
  outliers start: 18
  outliers final: 13
  residues processed: 242
  average time/residue: 1.4657
  time to fit residues: 389.0850
Evaluate side-chains
  249 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 234
  time to evaluate  : 1.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1532 MET
Chi-restraints excluded: chain B residue 1603 LEU
Chi-restraints excluded: chain B residue 1691 MET
Chi-restraints excluded: chain C residue 1582 MET
Chi-restraints excluded: chain D residue 1603 LEU
Chi-restraints excluded: chain D residue 1691 MET
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain L residue   60 VAL
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  169 LYS
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain E residue  201 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 14 optimal weight:    0.0570
   chunk 168 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 121 optimal weight:    5.9990
   chunk 191 optimal weight:    7.9990
   chunk 73 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1653 GLN
** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1653 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 = 0.145383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.080911 restraints weight = 26682.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.56
r_work: 0.2873 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16008  Z= 0.185
  Angle     :  0.602   9.450  21762  Z= 0.303
  Chirality :  0.041   0.169   2530
  Planarity :  0.004   0.058   2678
  Dihedral  :  4.267  24.765   2112
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 18.33 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.19), residues: 1944
  helix:  1.76 (0.17), residues: 936
  sheet:  0.04 (0.26), residues: 412
  loop : -0.35 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP F 163 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.010   0.001   PHE L 209 
 TYR   0.024   0.001   TYR B1591 
 ARG   0.007   0.000   ARG F 108 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16901.97 seconds
wall clock time: 304 minutes 5.90 seconds (18245.90 seconds total)