Starting phenix.real_space_refine
on Tue Jun 10 12:12:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c8k_16482/06_2025/8c8k_16482.cif"
  }
  resolution = 2.87
  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=   0.005
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       6      5.16       5
     C    7074      2.51       5
     N    1758      2.21       5
     O    2592      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 113 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11430
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
    Chain: "B"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
    Chain: "C"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
    Chain: "D"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
    Chain: "E"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
    Chain: "F"
      Number of atoms: 1905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1905
          Classifications: {'peptide': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244}
  Time building chain proxies: 7.66, per 1000 atoms: 0.67
  Number of scatterers: 11430
  At special positions: 0
  Unit cell: (243.516, 258.804, 49.14, 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       6     16.00
     O    2592      8.00
     N    1758      7.00
     C    7074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.73
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2724

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 30 sheets defined
      3.2% alpha, 50.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1389 through 1392
    Processing helix  chain 'A' and resid 1523 through 1526
    Processing helix  chain 'B' and resid 1389 through 1392
    Processing helix  chain 'B' and resid 1523 through 1526
    Processing helix  chain 'C' and resid 1389 through 1392
    Processing helix  chain 'C' and resid 1523 through 1526
    Processing helix  chain 'D' and resid 1389 through 1392
    Processing helix  chain 'D' and resid 1523 through 1526
    Processing helix  chain 'E' and resid 1389 through 1392
    Processing helix  chain 'E' and resid 1523 through 1526
    Processing helix  chain 'F' and resid 1389 through 1392
    Processing helix  chain 'F' and resid 1523 through 1526
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1368 through 1371
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1368 through 1371
      removed outlier: 3.869A  pdb=" N   GLY A1468 " --> pdb=" O   GLU A1436 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1375 through 1376
      removed outlier: 7.576A  pdb=" N   GLU A1488 " --> pdb=" O   PHE A1484 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE A1484 " --> pdb=" O   GLU A1488 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1502 through 1505
      removed outlier: 3.514A  pdb=" N   VAL A1518 " --> pdb=" O   GLY A1564 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A1564 " --> pdb=" O   VAL A1518 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   THR A1565 " --> pdb=" O   THR A1551 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   THR A1551 " --> pdb=" O   THR A1565 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   PHE A1567 " --> pdb=" O   ASP A1549 " (cutoff:3.500A)
      removed outlier: 10.644A  pdb=" N   ASP A1549 " --> pdb=" O   PHE A1567 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   GLU A1536 " --> pdb=" O   GLU A1592 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLU A1592 " --> pdb=" O   GLU A1536 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP A1585 " --> pdb=" O   ILE A1614 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A1614 " --> pdb=" O   ASP A1585 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU A1606 " --> pdb=" O   ASP A1593 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1502 through 1505
      removed outlier: 3.514A  pdb=" N   VAL A1518 " --> pdb=" O   GLY A1564 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A1564 " --> pdb=" O   VAL A1518 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   LEU A1579 " --> pdb=" O   THR A1565 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   PHE A1567 " --> pdb=" O   LEU A1579 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1368 through 1371
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1368 through 1371
      removed outlier: 3.863A  pdb=" N   GLY B1468 " --> pdb=" O   GLU B1436 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1375 through 1376
      removed outlier: 7.562A  pdb=" N   GLU B1488 " --> pdb=" O   PHE B1484 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE B1484 " --> pdb=" O   GLU B1488 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1502 through 1505
      removed outlier: 3.513A  pdb=" N   VAL B1518 " --> pdb=" O   GLY B1564 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY B1564 " --> pdb=" O   VAL B1518 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR B1565 " --> pdb=" O   THR B1551 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   THR B1551 " --> pdb=" O   THR B1565 " (cutoff:3.500A)
      removed outlier: 10.025A  pdb=" N   PHE B1567 " --> pdb=" O   ASP B1549 " (cutoff:3.500A)
      removed outlier: 10.670A  pdb=" N   ASP B1549 " --> pdb=" O   PHE B1567 " (cutoff:3.500A)
      removed outlier: 8.795A  pdb=" N   GLU B1536 " --> pdb=" O   GLU B1592 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLU B1592 " --> pdb=" O   GLU B1536 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP B1585 " --> pdb=" O   ILE B1614 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B1614 " --> pdb=" O   ASP B1585 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU B1606 " --> pdb=" O   ASP B1593 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1502 through 1505
      removed outlier: 3.513A  pdb=" N   VAL B1518 " --> pdb=" O   GLY B1564 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY B1564 " --> pdb=" O   VAL B1518 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   LEU B1579 " --> pdb=" O   THR B1565 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE B1567 " --> pdb=" O   LEU B1579 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 1368 through 1371
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1368 through 1371
      removed outlier: 3.865A  pdb=" N   GLY C1468 " --> pdb=" O   GLU C1436 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 1375 through 1376
      removed outlier: 7.555A  pdb=" N   GLU C1488 " --> pdb=" O   PHE C1484 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE C1484 " --> pdb=" O   GLU C1488 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 1502 through 1505
      removed outlier: 3.514A  pdb=" N   VAL C1518 " --> pdb=" O   GLY C1564 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY C1564 " --> pdb=" O   VAL C1518 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   THR C1565 " --> pdb=" O   THR C1551 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR C1551 " --> pdb=" O   THR C1565 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   PHE C1567 " --> pdb=" O   ASP C1549 " (cutoff:3.500A)
      removed outlier: 10.628A  pdb=" N   ASP C1549 " --> pdb=" O   PHE C1567 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   GLU C1536 " --> pdb=" O   GLU C1592 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   GLU C1592 " --> pdb=" O   GLU C1536 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP C1585 " --> pdb=" O   ILE C1614 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE C1614 " --> pdb=" O   ASP C1585 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU C1606 " --> pdb=" O   ASP C1593 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 1502 through 1505
      removed outlier: 3.514A  pdb=" N   VAL C1518 " --> pdb=" O   GLY C1564 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY C1564 " --> pdb=" O   VAL C1518 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   LEU C1579 " --> pdb=" O   THR C1565 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   PHE C1567 " --> pdb=" O   LEU C1579 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 1368 through 1371
    Processing sheet with id=AB8, first strand: chain 'D' and resid 1368 through 1371
      removed outlier: 3.868A  pdb=" N   GLY D1468 " --> pdb=" O   GLU D1436 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 1375 through 1376
      removed outlier: 7.561A  pdb=" N   GLU D1488 " --> pdb=" O   PHE D1484 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE D1484 " --> pdb=" O   GLU D1488 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 1502 through 1505
      removed outlier: 3.515A  pdb=" N   VAL D1518 " --> pdb=" O   GLY D1564 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY D1564 " --> pdb=" O   VAL D1518 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   THR D1565 " --> pdb=" O   THR D1551 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   THR D1551 " --> pdb=" O   THR D1565 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   PHE D1567 " --> pdb=" O   ASP D1549 " (cutoff:3.500A)
      removed outlier: 10.648A  pdb=" N   ASP D1549 " --> pdb=" O   PHE D1567 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   GLU D1536 " --> pdb=" O   GLU D1592 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLU D1592 " --> pdb=" O   GLU D1536 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP D1585 " --> pdb=" O   ILE D1614 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE D1614 " --> pdb=" O   ASP D1585 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU D1606 " --> pdb=" O   ASP D1593 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 1502 through 1505
      removed outlier: 3.515A  pdb=" N   VAL D1518 " --> pdb=" O   GLY D1564 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY D1564 " --> pdb=" O   VAL D1518 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   LEU D1579 " --> pdb=" O   THR D1565 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   PHE D1567 " --> pdb=" O   LEU D1579 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 1368 through 1371
    Processing sheet with id=AC4, first strand: chain 'E' and resid 1368 through 1371
      removed outlier: 3.864A  pdb=" N   GLY E1468 " --> pdb=" O   GLU E1436 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 1375 through 1376
      removed outlier: 7.562A  pdb=" N   GLU E1488 " --> pdb=" O   PHE E1484 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE E1484 " --> pdb=" O   GLU E1488 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 1502 through 1505
      removed outlier: 3.516A  pdb=" N   VAL E1518 " --> pdb=" O   GLY E1564 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY E1564 " --> pdb=" O   VAL E1518 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR E1565 " --> pdb=" O   THR E1551 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   THR E1551 " --> pdb=" O   THR E1565 " (cutoff:3.500A)
      removed outlier: 10.012A  pdb=" N   PHE E1567 " --> pdb=" O   ASP E1549 " (cutoff:3.500A)
      removed outlier: 10.627A  pdb=" N   ASP E1549 " --> pdb=" O   PHE E1567 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   GLU E1536 " --> pdb=" O   GLU E1592 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   GLU E1592 " --> pdb=" O   GLU E1536 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP E1585 " --> pdb=" O   ILE E1614 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE E1614 " --> pdb=" O   ASP E1585 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU E1606 " --> pdb=" O   ASP E1593 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 1502 through 1505
      removed outlier: 3.516A  pdb=" N   VAL E1518 " --> pdb=" O   GLY E1564 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY E1564 " --> pdb=" O   VAL E1518 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   LEU E1579 " --> pdb=" O   THR E1565 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   PHE E1567 " --> pdb=" O   LEU E1579 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 1368 through 1371
    Processing sheet with id=AC9, first strand: chain 'F' and resid 1368 through 1371
      removed outlier: 3.865A  pdb=" N   GLY F1468 " --> pdb=" O   GLU F1436 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 1375 through 1376
      removed outlier: 7.555A  pdb=" N   GLU F1488 " --> pdb=" O   PHE F1484 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   PHE F1484 " --> pdb=" O   GLU F1488 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'F' and resid 1502 through 1505
      removed outlier: 3.513A  pdb=" N   VAL F1518 " --> pdb=" O   GLY F1564 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY F1564 " --> pdb=" O   VAL F1518 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   THR F1565 " --> pdb=" O   THR F1551 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   THR F1551 " --> pdb=" O   THR F1565 " (cutoff:3.500A)
      removed outlier: 10.016A  pdb=" N   PHE F1567 " --> pdb=" O   ASP F1549 " (cutoff:3.500A)
      removed outlier: 10.634A  pdb=" N   ASP F1549 " --> pdb=" O   PHE F1567 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   GLU F1536 " --> pdb=" O   GLU F1592 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   GLU F1592 " --> pdb=" O   GLU F1536 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP F1585 " --> pdb=" O   ILE F1614 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE F1614 " --> pdb=" O   ASP F1585 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU F1606 " --> pdb=" O   ASP F1593 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 1502 through 1505
      removed outlier: 3.513A  pdb=" N   VAL F1518 " --> pdb=" O   GLY F1564 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY F1564 " --> pdb=" O   VAL F1518 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   LEU F1579 " --> pdb=" O   THR F1565 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   PHE F1567 " --> pdb=" O   LEU F1579 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1278 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: 4.67

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 2224
        1.26 -     1.41: 2617
        1.41 -     1.55: 6785
        1.55 -     1.69: 2
        1.69 -     1.83: 12
  Bond restraints: 11640
  Sorted by residual:
  bond pdb=" C   THR A1428 "
       pdb=" O   THR A1428 "
    ideal  model  delta    sigma   weight residual
    1.237  1.134  0.102 1.19e-02 7.06e+03 7.38e+01
  bond pdb=" C   LEU E1397 "
       pdb=" O   LEU E1397 "
    ideal  model  delta    sigma   weight residual
    1.234  1.136  0.098 1.18e-02 7.18e+03 6.95e+01
  bond pdb=" C   LEU B1397 "
       pdb=" O   LEU B1397 "
    ideal  model  delta    sigma   weight residual
    1.234  1.138  0.097 1.18e-02 7.18e+03 6.70e+01
  bond pdb=" C   THR D1428 "
       pdb=" O   THR D1428 "
    ideal  model  delta    sigma   weight residual
    1.237  1.142  0.095 1.19e-02 7.06e+03 6.35e+01
  bond pdb=" C   LEU F1397 "
       pdb=" O   LEU F1397 "
    ideal  model  delta    sigma   weight residual
    1.234  1.143  0.092 1.18e-02 7.18e+03 6.02e+01
  ... (remaining 11635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 14072
        2.30 -     4.59: 1782
        4.59 -     6.89: 89
        6.89 -     9.19: 1
        9.19 -    11.48: 4
  Bond angle restraints: 15948
  Sorted by residual:
  angle pdb=" CG  ARG B1578 "
        pdb=" CD  ARG B1578 "
        pdb=" NE  ARG B1578 "
      ideal   model   delta    sigma   weight residual
     112.00  100.52   11.48 2.20e+00 2.07e-01 2.72e+01
  angle pdb=" CG  ARG D1578 "
        pdb=" CD  ARG D1578 "
        pdb=" NE  ARG D1578 "
      ideal   model   delta    sigma   weight residual
     112.00  100.85   11.15 2.20e+00 2.07e-01 2.57e+01
  angle pdb=" CG  ARG A1578 "
        pdb=" CD  ARG A1578 "
        pdb=" NE  ARG A1578 "
      ideal   model   delta    sigma   weight residual
     112.00  100.89   11.11 2.20e+00 2.07e-01 2.55e+01
  angle pdb=" CA  GLY B1427 "
        pdb=" C   GLY B1427 "
        pdb=" N   THR B1428 "
      ideal   model   delta    sigma   weight residual
     114.50  120.16   -5.66 1.19e+00 7.06e-01 2.26e+01
  angle pdb=" CA  GLY E1427 "
        pdb=" C   GLY E1427 "
        pdb=" N   THR E1428 "
      ideal   model   delta    sigma   weight residual
     114.50  120.12   -5.62 1.19e+00 7.06e-01 2.23e+01
  ... (remaining 15943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.05: 5772
       13.05 -    26.09: 634
       26.09 -    39.14: 240
       39.14 -    52.18: 32
       52.18 -    65.23: 24
  Dihedral angle restraints: 6702
    sinusoidal: 2430
      harmonic: 4272
  Sorted by residual:
  dihedral pdb=" CA  PRO A1408 "
           pdb=" C   PRO A1408 "
           pdb=" N   ILE A1409 "
           pdb=" CA  ILE A1409 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.00   19.00     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  PRO E1408 "
           pdb=" C   PRO E1408 "
           pdb=" N   ILE E1409 "
           pdb=" CA  ILE E1409 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  PRO F1408 "
           pdb=" C   PRO F1408 "
           pdb=" N   ILE F1409 "
           pdb=" CA  ILE F1409 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 6699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 820
       0.051 -    0.101: 618
       0.101 -    0.152: 353
       0.152 -    0.202: 86
       0.202 -    0.253: 7
  Chirality restraints: 1884
  Sorted by residual:
  chirality pdb=" CA  PHE E1365 "
            pdb=" N   PHE E1365 "
            pdb=" C   PHE E1365 "
            pdb=" CB  PHE E1365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  PHE B1365 "
            pdb=" N   PHE B1365 "
            pdb=" C   PHE B1365 "
            pdb=" CB  PHE B1365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  PHE C1365 "
            pdb=" N   PHE C1365 "
            pdb=" C   PHE C1365 "
            pdb=" CB  PHE C1365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1881 not shown)

  Planarity restraints: 2130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D1393 "   -0.013 2.00e-02 2.50e+03   3.99e-02 2.79e+01
        pdb=" CG  PHE D1393 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE D1393 "    0.074 2.00e-02 2.50e+03
        pdb=" CD2 PHE D1393 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 PHE D1393 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE2 PHE D1393 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE D1393 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D1394 "    0.017 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" CG  ASP D1394 "   -0.063 2.00e-02 2.50e+03
        pdb=" OD1 ASP D1394 "    0.023 2.00e-02 2.50e+03
        pdb=" OD2 ASP D1394 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A1394 "   -0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" CG  ASP A1394 "    0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASP A1394 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD2 ASP A1394 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 2127 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1962
        2.79 -     3.32: 11332
        3.32 -     3.84: 17802
        3.84 -     4.37: 22906
        4.37 -     4.90: 38132
  Nonbonded interactions: 92134
  Sorted by model distance:
  nonbonded pdb=" OG  SER F1574 "
            pdb=" N   ARG F1580 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER E1574 "
            pdb=" N   ARG E1580 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OG  SER D1574 "
            pdb=" N   ARG D1580 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OG  SER B1574 "
            pdb=" N   ARG B1580 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OG  SER C1574 "
            pdb=" N   ARG C1580 "
     model   vdw
     2.268 3.120
  ... (remaining 92129 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  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:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.400
  Find NCS groups from input model:        0.440
  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:             0.010
  Load rotamer database and sin/cos tables:15.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
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      :  0.013   0.124  11640  Z= 0.969
  Angle     :  1.500  11.483  15948  Z= 1.048
  Chirality :  0.081   0.253   1884
  Planarity :  0.006   0.075   2130
  Dihedral  : 13.311  65.228   3978
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.48 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.75 (0.18), residues: 1506
  helix: -3.34 (0.64), residues: 36
  sheet: -0.33 (0.20), residues: 528
  loop : -1.64 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.006   TRP B1378 
 HIS   0.029   0.008   HIS B1577 
 PHE   0.074   0.006   PHE D1393 
 TYR   0.036   0.005   TYR A1383 
 ARG   0.019   0.002   ARG D1578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24019 (  378)
  hydrogen bonds       : angle       8.12836 ( 1278)
  covalent geometry    : bond        0.01311 (11640)
  covalent geometry    : angle       1.49971 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 267
  time to evaluate  : 1.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1405 ASP cc_start: 0.7128 (m-30) cc_final: 0.6917 (m-30)
REVERT: A 1590 GLU cc_start: 0.6782 (pt0) cc_final: 0.6543 (pp20)
REVERT: A 1608 ILE cc_start: 0.6487 (mm) cc_final: 0.6251 (mt)
REVERT: B 1407 ASP cc_start: 0.6723 (t70) cc_final: 0.6137 (p0)
REVERT: B 1419 ASP cc_start: 0.7725 (p0) cc_final: 0.7374 (t0)
REVERT: B 1497 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6464 (ptp-170)
REVERT: B 1596 LEU cc_start: 0.7154 (tp) cc_final: 0.6951 (mt)
REVERT: C 1407 ASP cc_start: 0.6931 (t70) cc_final: 0.6499 (p0)
REVERT: C 1476 ASP cc_start: 0.7408 (t0) cc_final: 0.6892 (t0)
REVERT: C 1486 GLU cc_start: 0.6305 (tt0) cc_final: 0.6004 (pm20)
REVERT: C 1497 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6861 (ptp-170)
REVERT: C 1504 GLN cc_start: 0.6664 (pt0) cc_final: 0.6296 (pt0)
REVERT: D 1405 ASP cc_start: 0.7347 (m-30) cc_final: 0.7113 (m-30)
REVERT: D 1452 ASN cc_start: 0.5764 (p0) cc_final: 0.5387 (p0)
REVERT: D 1590 GLU cc_start: 0.6783 (pt0) cc_final: 0.6516 (pp20)
REVERT: D 1608 ILE cc_start: 0.6406 (mm) cc_final: 0.6179 (mt)
REVERT: E 1407 ASP cc_start: 0.6718 (t70) cc_final: 0.6134 (p0)
REVERT: E 1419 ASP cc_start: 0.7725 (p0) cc_final: 0.7373 (t0)
REVERT: E 1497 ARG cc_start: 0.6846 (mtm110) cc_final: 0.6462 (ptp-170)
REVERT: E 1510 TYR cc_start: 0.6661 (m-80) cc_final: 0.5995 (m-80)
REVERT: F 1407 ASP cc_start: 0.6942 (t70) cc_final: 0.6514 (p0)
REVERT: F 1476 ASP cc_start: 0.7407 (t0) cc_final: 0.6865 (t0)
REVERT: F 1486 GLU cc_start: 0.6331 (tt0) cc_final: 0.6011 (pm20)
REVERT: F 1497 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6861 (ptp-170)
  outliers start: 8
  outliers final: 2
  residues processed: 275
  average time/residue: 1.1878
  time to fit residues: 352.8175
Evaluate side-chains
  155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1575 SER
Chi-restraints excluded: chain D residue 1575 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 113 optimal weight:   10.0000
   chunk 63 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 117 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 71 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 136 optimal weight:    5.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
A1594 ASN
B1373 GLN
B1391 HIS
B1594 ASN
C1373 GLN
C1391 HIS
C1577 HIS
C1594 ASN
D1594 ASN
E1373 GLN
E1391 HIS
E1577 HIS
E1594 ASN
F1373 GLN
F1391 HIS
F1577 HIS
F1594 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.140286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.126486 restraints weight = 18415.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.55
r_work: 0.3724 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  11640  Z= 0.202
  Angle     :  0.688   5.807  15948  Z= 0.383
  Chirality :  0.052   0.165   1884
  Planarity :  0.005   0.048   2130
  Dihedral  :  5.542  17.263   1580
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 10.85 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.56 (0.18), residues: 1506
  helix: -3.05 (0.32), residues: 72
  sheet:  0.07 (0.20), residues: 522
  loop : -1.60 (0.17), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B1378 
 HIS   0.004   0.002   HIS E1577 
 PHE   0.022   0.003   PHE E1442 
 TYR   0.011   0.003   TYR B1600 
 ARG   0.005   0.001   ARG B1578 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  378)
  hydrogen bonds       : angle       5.85279 ( 1278)
  covalent geometry    : bond        0.00473 (11640)
  covalent geometry    : angle       0.68820 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 155
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1405 ASP cc_start: 0.7172 (m-30) cc_final: 0.6896 (m-30)
REVERT: A 1590 GLU cc_start: 0.7011 (pt0) cc_final: 0.6778 (pp20)
REVERT: B 1410 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8006 (ttmt)
REVERT: B 1573 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7209 (pt0)
REVERT: B 1596 LEU cc_start: 0.7764 (tp) cc_final: 0.7481 (mt)
REVERT: C 1486 GLU cc_start: 0.7417 (tt0) cc_final: 0.7076 (pm20)
REVERT: C 1577 HIS cc_start: 0.7900 (m90) cc_final: 0.7562 (m-70)
REVERT: D 1405 ASP cc_start: 0.7212 (m-30) cc_final: 0.6944 (m-30)
REVERT: D 1410 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8300 (ttmt)
REVERT: D 1590 GLU cc_start: 0.7002 (pt0) cc_final: 0.6766 (pp20)
REVERT: E 1410 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8003 (ttmt)
REVERT: E 1573 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7151 (pt0)
REVERT: E 1596 LEU cc_start: 0.7839 (mt) cc_final: 0.7583 (mt)
REVERT: F 1486 GLU cc_start: 0.7425 (tt0) cc_final: 0.7066 (pm20)
REVERT: F 1577 HIS cc_start: 0.7825 (m90) cc_final: 0.7615 (m170)
  outliers start: 38
  outliers final: 14
  residues processed: 182
  average time/residue: 0.9661
  time to fit residues: 194.1285
Evaluate side-chains
  137 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1518 VAL
Chi-restraints excluded: chain A residue 1601 THR
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1601 THR
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1601 THR
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1410 LYS
Chi-restraints excluded: chain D residue 1518 VAL
Chi-restraints excluded: chain D residue 1601 THR
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1601 THR
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1601 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0980
   chunk 128 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0030
   chunk 144 optimal weight:    0.4980
   chunk 4 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    0.8792

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

Flipped N/Q/H residues before XYZ refinement:
A1391 HIS
A1452 ASN
A1594 ASN
B1452 ASN
B1594 ASN
C1452 ASN
C1594 ASN
D1391 HIS
D1594 ASN
E1452 ASN
E1594 ASN
F1594 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.145470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.131472 restraints weight = 18632.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.64
r_work: 0.3790 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11640  Z= 0.098
  Angle     :  0.534   4.892  15948  Z= 0.294
  Chirality :  0.046   0.166   1884
  Planarity :  0.003   0.038   2130
  Dihedral  :  4.649  15.447   1578
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.41 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: 1506
  helix: -2.42 (0.41), residues: 72
  sheet:  0.77 (0.19), residues: 588
  loop : -1.76 (0.18), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F1540 
 HIS   0.002   0.001   HIS E1391 
 PHE   0.008   0.001   PHE D1567 
 TYR   0.011   0.002   TYR A1383 
 ARG   0.009   0.001   ARG C1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  378)
  hydrogen bonds       : angle       5.14292 ( 1278)
  covalent geometry    : bond        0.00204 (11640)
  covalent geometry    : angle       0.53378 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 1577 HIS cc_start: 0.7782 (m90) cc_final: 0.7353 (m-70)
REVERT: E 1596 LEU cc_start: 0.7711 (mt) cc_final: 0.7454 (mt)
REVERT: E 1613 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6600 (pp)
REVERT: F 1486 GLU cc_start: 0.7231 (tt0) cc_final: 0.6985 (pm20)
REVERT: F 1577 HIS cc_start: 0.7713 (m90) cc_final: 0.7245 (m-70)
  outliers start: 22
  outliers final: 8
  residues processed: 156
  average time/residue: 0.6905
  time to fit residues: 124.0505
Evaluate side-chains
  130 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain B residue 1536 GLU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1452 ASN
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain E residue 1452 ASN
Chi-restraints excluded: chain E residue 1536 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 86 optimal weight:   20.0000
   chunk 97 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0980
   chunk 61 optimal weight:   20.0000
   chunk 109 optimal weight:    3.9990
   chunk 114 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    4.6188

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
A1594 ASN
B1577 HIS
B1594 ASN
C1594 ASN
D1594 ASN
E1594 ASN
F1594 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.140974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.127038 restraints weight = 18536.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 1.58
r_work: 0.3720 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3623 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11640  Z= 0.166
  Angle     :  0.630   6.515  15948  Z= 0.344
  Chirality :  0.051   0.175   1884
  Planarity :  0.004   0.033   2130
  Dihedral  :  5.088  15.355   1578
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.27 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.27 (0.19), residues: 1506
  helix: -2.59 (0.39), residues: 72
  sheet:  0.36 (0.19), residues: 546
  loop : -1.54 (0.18), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F1378 
 HIS   0.003   0.001   HIS C1391 
 PHE   0.017   0.003   PHE E1442 
 TYR   0.013   0.002   TYR D1383 
 ARG   0.008   0.001   ARG C1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  378)
  hydrogen bonds       : angle       5.48630 ( 1278)
  covalent geometry    : bond        0.00388 (11640)
  covalent geometry    : angle       0.62980 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 123
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1410 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8380 (ttmt)
REVERT: A 1476 ASP cc_start: 0.8000 (t0) cc_final: 0.7792 (t0)
REVERT: A 1613 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6881 (pp)
REVERT: B 1410 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8084 (ttmt)
REVERT: B 1419 ASP cc_start: 0.7318 (p0) cc_final: 0.7091 (p0)
REVERT: B 1573 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7154 (pt0)
REVERT: B 1596 LEU cc_start: 0.7817 (mt) cc_final: 0.7536 (mt)
REVERT: B 1613 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7045 (pp)
REVERT: C 1476 ASP cc_start: 0.7914 (t0) cc_final: 0.7484 (t0)
REVERT: C 1613 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6840 (pp)
REVERT: D 1476 ASP cc_start: 0.7988 (t0) cc_final: 0.7777 (t0)
REVERT: D 1613 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6898 (pp)
REVERT: E 1410 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8093 (ttmt)
REVERT: E 1419 ASP cc_start: 0.7366 (p0) cc_final: 0.7130 (p0)
REVERT: E 1573 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6966 (pt0)
REVERT: E 1596 LEU cc_start: 0.7799 (mt) cc_final: 0.7572 (mt)
REVERT: E 1613 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7019 (pp)
REVERT: F 1476 ASP cc_start: 0.7933 (t0) cc_final: 0.7543 (t0)
REVERT: F 1486 GLU cc_start: 0.7344 (tt0) cc_final: 0.6740 (pm20)
REVERT: F 1613 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6837 (pp)
  outliers start: 50
  outliers final: 26
  residues processed: 155
  average time/residue: 0.8238
  time to fit residues: 143.5093
Evaluate side-chains
  151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 114
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1410 LYS
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1518 VAL
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1613 LEU
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1518 VAL
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1536 GLU
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1518 VAL
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1601 THR
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1518 VAL
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1613 LEU
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1518 VAL
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1518 VAL
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1601 THR
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 86 optimal weight:   20.0000
   chunk 145 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 118 optimal weight:    8.9990
   chunk 113 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A1594 ASN
B1452 ASN
B1594 ASN
C1577 HIS
C1594 ASN
D1594 ASN
E1594 ASN
F1452 ASN
F1577 HIS
F1594 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.139115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.124983 restraints weight = 18463.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.62
r_work: 0.3697 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3599 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11640  Z= 0.218
  Angle     :  0.698   6.971  15948  Z= 0.382
  Chirality :  0.053   0.180   1884
  Planarity :  0.004   0.048   2130
  Dihedral  :  5.502  16.572   1578
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.92 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.51 (0.18), residues: 1506
  helix: -2.95 (0.38), residues: 72
  sheet:  0.22 (0.20), residues: 546
  loop : -1.70 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E1378 
 HIS   0.003   0.001   HIS F1391 
 PHE   0.020   0.003   PHE A1442 
 TYR   0.015   0.002   TYR D1383 
 ARG   0.010   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  378)
  hydrogen bonds       : angle       5.78267 ( 1278)
  covalent geometry    : bond        0.00516 (11640)
  covalent geometry    : angle       0.69815 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 119
  time to evaluate  : 1.261 
Fit side-chains
REVERT: A 1446 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7446 (t70)
REVERT: A 1476 ASP cc_start: 0.8088 (t0) cc_final: 0.7872 (t0)
REVERT: A 1567 PHE cc_start: 0.4919 (OUTLIER) cc_final: 0.4444 (m-80)
REVERT: B 1410 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8173 (ttmt)
REVERT: B 1573 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7222 (pt0)
REVERT: B 1596 LEU cc_start: 0.7849 (mt) cc_final: 0.7565 (mt)
REVERT: B 1613 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7089 (pp)
REVERT: C 1613 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7162 (pp)
REVERT: D 1446 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7408 (t70)
REVERT: D 1476 ASP cc_start: 0.8074 (t0) cc_final: 0.7861 (t0)
REVERT: D 1486 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6566 (pm20)
REVERT: D 1567 PHE cc_start: 0.4996 (OUTLIER) cc_final: 0.4472 (m-80)
REVERT: E 1410 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8184 (ttmt)
REVERT: E 1573 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7137 (pt0)
REVERT: E 1596 LEU cc_start: 0.7840 (mt) cc_final: 0.7632 (mt)
REVERT: E 1613 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7071 (pp)
REVERT: F 1613 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7166 (pp)
  outliers start: 64
  outliers final: 38
  residues processed: 161
  average time/residue: 0.8140
  time to fit residues: 147.6201
Evaluate side-chains
  158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 107
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1378 TRP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1446 ASP
Chi-restraints excluded: chain A residue 1518 VAL
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1405 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1518 VAL
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1601 THR
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1378 TRP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1518 VAL
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1601 THR
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1446 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1518 VAL
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1405 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1518 VAL
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1601 THR
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1378 TRP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1452 ASN
Chi-restraints excluded: chain F residue 1518 VAL
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1601 THR
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 131 optimal weight:    2.9990
   chunk 134 optimal weight:   20.0000
   chunk 62 optimal weight:    0.0170
   chunk 74 optimal weight:   20.0000
   chunk 122 optimal weight:    8.9990
   overall best weight:    6.2026

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
A1594 ASN
B1594 ASN
C1594 ASN
D1594 ASN
E1594 ASN
F1594 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.138844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.124748 restraints weight = 18732.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.63
r_work: 0.3695 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  11640  Z= 0.205
  Angle     :  0.677   6.719  15948  Z= 0.370
  Chirality :  0.052   0.177   1884
  Planarity :  0.004   0.035   2130
  Dihedral  :  5.451  16.387   1578
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 18.63 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.59 (0.18), residues: 1506
  helix: -3.04 (0.38), residues: 72
  sheet:  0.20 (0.20), residues: 546
  loop : -1.78 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1378 
 HIS   0.003   0.001   HIS C1391 
 PHE   0.018   0.003   PHE A1442 
 TYR   0.015   0.002   TYR D1383 
 ARG   0.007   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04246 (  378)
  hydrogen bonds       : angle       5.73915 ( 1278)
  covalent geometry    : bond        0.00487 (11640)
  covalent geometry    : angle       0.67658 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 103
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A 1476 ASP cc_start: 0.8073 (t0) cc_final: 0.7871 (t0)
REVERT: A 1567 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.4482 (m-80)
REVERT: A 1613 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7097 (pp)
REVERT: B 1573 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7160 (pt0)
REVERT: B 1613 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6847 (pp)
REVERT: C 1613 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7005 (pp)
REVERT: D 1446 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7349 (t70)
REVERT: D 1476 ASP cc_start: 0.8068 (t0) cc_final: 0.7864 (t0)
REVERT: D 1486 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6579 (pm20)
REVERT: D 1567 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.4485 (m-80)
REVERT: D 1613 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7066 (pp)
REVERT: E 1573 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7236 (pt0)
REVERT: E 1613 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6785 (pp)
REVERT: F 1476 ASP cc_start: 0.7985 (t0) cc_final: 0.7477 (t0)
REVERT: F 1613 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6898 (pp)
  outliers start: 59
  outliers final: 33
  residues processed: 142
  average time/residue: 0.9301
  time to fit residues: 149.5538
Evaluate side-chains
  146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 101
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain A residue 1613 LEU
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1405 ASP
Chi-restraints excluded: chain B residue 1518 VAL
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1524 ASP
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1518 VAL
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1601 THR
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1446 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain D residue 1613 LEU
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1405 ASP
Chi-restraints excluded: chain E residue 1518 VAL
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1524 ASP
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1518 VAL
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1601 THR
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 119 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 81 optimal weight:    9.9990
   chunk 108 optimal weight:   20.0000
   chunk 149 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
B1594 ASN
C1452 ASN
C1594 ASN
D1594 ASN
E1452 ASN
E1594 ASN
F1594 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.138838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.124660 restraints weight = 18977.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.65
r_work: 0.3695 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  11640  Z= 0.200
  Angle     :  0.669   6.745  15948  Z= 0.366
  Chirality :  0.052   0.176   1884
  Planarity :  0.004   0.034   2130
  Dihedral  :  5.442  16.584   1578
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 19.26 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.64 (0.18), residues: 1506
  helix: -3.09 (0.39), residues: 72
  sheet:  0.21 (0.20), residues: 546
  loop : -1.85 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A1378 
 HIS   0.003   0.001   HIS C1391 
 PHE   0.018   0.003   PHE A1442 
 TYR   0.015   0.002   TYR A1383 
 ARG   0.007   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  378)
  hydrogen bonds       : angle       5.74291 ( 1278)
  covalent geometry    : bond        0.00474 (11640)
  covalent geometry    : angle       0.66919 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 110
  time to evaluate  : 1.356 
Fit side-chains
REVERT: A 1567 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.4470 (m-80)
REVERT: A 1613 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7047 (pp)
REVERT: B 1410 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8195 (ttmt)
REVERT: B 1573 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7182 (pt0)
REVERT: B 1613 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6731 (pp)
REVERT: C 1594 ASN cc_start: 0.7058 (m-40) cc_final: 0.6135 (m110)
REVERT: C 1605 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.4896 (mm-30)
REVERT: C 1613 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6846 (pp)
REVERT: D 1410 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8409 (ttmt)
REVERT: D 1446 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7378 (t70)
REVERT: D 1486 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6591 (pm20)
REVERT: D 1567 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4495 (m-80)
REVERT: D 1613 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7033 (pp)
REVERT: E 1410 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8202 (ttmt)
REVERT: E 1573 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7203 (pt0)
REVERT: E 1613 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6725 (pp)
REVERT: F 1476 ASP cc_start: 0.7975 (t0) cc_final: 0.7458 (t0)
REVERT: F 1594 ASN cc_start: 0.7049 (m-40) cc_final: 0.6155 (m110)
REVERT: F 1605 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5065 (mm-30)
REVERT: F 1613 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6832 (pp)
  outliers start: 65
  outliers final: 35
  residues processed: 151
  average time/residue: 0.8035
  time to fit residues: 136.9331
Evaluate side-chains
  159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 107
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain A residue 1613 LEU
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1518 VAL
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1524 ASP
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1378 TRP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1452 ASN
Chi-restraints excluded: chain C residue 1518 VAL
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1601 THR
Chi-restraints excluded: chain C residue 1605 GLU
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1410 LYS
Chi-restraints excluded: chain D residue 1446 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain D residue 1613 LEU
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1452 ASN
Chi-restraints excluded: chain E residue 1518 VAL
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1524 ASP
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1378 TRP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1518 VAL
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1601 THR
Chi-restraints excluded: chain F residue 1605 GLU
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 97 optimal weight:    1.9990
   chunk 34 optimal weight:   20.0000
   chunk 110 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0970
   chunk 32 optimal weight:    7.9990
   overall best weight:    3.6186

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

Flipped N/Q/H residues before XYZ refinement:
A1594 ASN
E1452 ASN
F1452 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.140668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.126563 restraints weight = 18778.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 1.64
r_work: 0.3721 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  11640  Z= 0.142
  Angle     :  0.603   5.915  15948  Z= 0.330
  Chirality :  0.049   0.173   1884
  Planarity :  0.003   0.034   2130
  Dihedral  :  5.156  15.882   1578
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.46 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.53 (0.19), residues: 1506
  helix: -3.02 (0.39), residues: 72
  sheet:  0.29 (0.20), residues: 546
  loop : -1.78 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C1378 
 HIS   0.002   0.001   HIS F1391 
 PHE   0.014   0.002   PHE B1442 
 TYR   0.013   0.002   TYR D1383 
 ARG   0.006   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  378)
  hydrogen bonds       : angle       5.49757 ( 1278)
  covalent geometry    : bond        0.00328 (11640)
  covalent geometry    : angle       0.60329 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A 1410 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8275 (ttmt)
REVERT: A 1567 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.4541 (m-80)
REVERT: B 1410 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8393 (ttmt)
REVERT: B 1613 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6626 (pp)
REVERT: C 1476 ASP cc_start: 0.7905 (t0) cc_final: 0.7386 (t0)
REVERT: C 1613 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6668 (pp)
REVERT: D 1446 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7378 (t70)
REVERT: D 1486 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6714 (pm20)
REVERT: D 1567 PHE cc_start: 0.4897 (OUTLIER) cc_final: 0.4455 (m-80)
REVERT: E 1410 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8400 (ttmt)
REVERT: E 1613 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6632 (pp)
REVERT: F 1476 ASP cc_start: 0.7917 (t0) cc_final: 0.7468 (t0)
REVERT: F 1613 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6613 (pp)
  outliers start: 44
  outliers final: 27
  residues processed: 138
  average time/residue: 0.7535
  time to fit residues: 118.5012
Evaluate side-chains
  147 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1410 LYS
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1524 ASP
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1378 TRP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1446 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1452 ASN
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1378 TRP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1452 ASN
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 132 optimal weight:    9.9990
   chunk 113 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 58 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 148 optimal weight:    0.0270
   overall best weight:    6.2046

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
B1594 ASN
C1452 ASN
C1594 ASN
D1594 ASN
E1452 ASN
E1594 ASN
F1594 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.138843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.124714 restraints weight = 18863.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.64
r_work: 0.3694 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  11640  Z= 0.204
  Angle     :  0.675   6.849  15948  Z= 0.369
  Chirality :  0.052   0.176   1884
  Planarity :  0.004   0.037   2130
  Dihedral  :  5.413  16.528   1578
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 20.68 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.67 (0.18), residues: 1506
  helix: -3.13 (0.39), residues: 72
  sheet:  0.19 (0.20), residues: 546
  loop : -1.87 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E1378 
 HIS   0.003   0.001   HIS D1391 
 PHE   0.019   0.003   PHE A1442 
 TYR   0.015   0.002   TYR D1383 
 ARG   0.006   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  378)
  hydrogen bonds       : angle       5.72520 ( 1278)
  covalent geometry    : bond        0.00486 (11640)
  covalent geometry    : angle       0.67453 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 106
  time to evaluate  : 1.235 
Fit side-chains
REVERT: A 1410 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8329 (ttmt)
REVERT: A 1446 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7441 (t70)
REVERT: A 1567 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.4387 (m-80)
REVERT: B 1410 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8184 (ttmt)
REVERT: B 1573 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (pt0)
REVERT: B 1613 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6691 (pp)
REVERT: C 1605 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.4917 (mm-30)
REVERT: C 1613 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6810 (pp)
REVERT: D 1410 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8320 (ttmt)
REVERT: D 1446 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7370 (t70)
REVERT: D 1486 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6666 (pm20)
REVERT: D 1567 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4489 (m-80)
REVERT: E 1410 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8193 (ttmt)
REVERT: E 1573 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7287 (pt0)
REVERT: E 1613 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6665 (pp)
REVERT: F 1476 ASP cc_start: 0.7956 (t0) cc_final: 0.7429 (t0)
REVERT: F 1605 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.4809 (mm-30)
REVERT: F 1613 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6771 (pp)
  outliers start: 60
  outliers final: 30
  residues processed: 142
  average time/residue: 0.8318
  time to fit residues: 132.7178
Evaluate side-chains
  152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 105
  time to evaluate  : 1.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1410 LYS
Chi-restraints excluded: chain A residue 1446 ASP
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1476 ASP
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1524 ASP
Chi-restraints excluded: chain B residue 1573 GLU
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1452 ASN
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1605 GLU
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1398 VAL
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1410 LYS
Chi-restraints excluded: chain D residue 1446 ASP
Chi-restraints excluded: chain D residue 1476 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1452 ASN
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1524 ASP
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1605 GLU
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 140 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 93 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
A1594 ASN
C1452 ASN
D1594 ASN
E1452 ASN
F1452 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.139603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.125602 restraints weight = 18646.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 1.62
r_work: 0.3706 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  11640  Z= 0.174
  Angle     :  0.644   6.399  15948  Z= 0.353
  Chirality :  0.050   0.175   1884
  Planarity :  0.004   0.036   2130
  Dihedral  :  5.299  16.138   1578
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 21.38 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.65 (0.19), residues: 1506
  helix: -3.14 (0.39), residues: 72
  sheet:  0.19 (0.20), residues: 546
  loop : -1.84 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1378 
 HIS   0.003   0.001   HIS A1391 
 PHE   0.016   0.003   PHE B1484 
 TYR   0.014   0.002   TYR D1383 
 ARG   0.006   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  378)
  hydrogen bonds       : angle       5.62418 ( 1278)
  covalent geometry    : bond        0.00410 (11640)
  covalent geometry    : angle       0.64410 (15948)

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

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

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3012 Ramachandran restraints generated.
    1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 110
  time to evaluate  : 1.197 
Fit side-chains
REVERT: A 1410 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8298 (ttmt)
REVERT: A 1567 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4467 (m-80)
REVERT: B 1410 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8183 (ttmt)
REVERT: B 1613 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6628 (pp)
REVERT: C 1476 ASP cc_start: 0.7910 (t0) cc_final: 0.7383 (t0)
REVERT: C 1605 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.4911 (mm-30)
REVERT: C 1613 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6769 (pp)
REVERT: D 1410 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8318 (ttmt)
REVERT: D 1486 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6672 (pm20)
REVERT: D 1567 PHE cc_start: 0.4947 (OUTLIER) cc_final: 0.4507 (m-80)
REVERT: E 1410 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8187 (ttmt)
REVERT: E 1573 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7286 (pt0)
REVERT: E 1613 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6620 (pp)
REVERT: F 1476 ASP cc_start: 0.7933 (t0) cc_final: 0.7415 (t0)
REVERT: F 1605 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.4722 (mm-30)
REVERT: F 1613 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6693 (pp)
  outliers start: 52
  outliers final: 32
  residues processed: 139
  average time/residue: 0.8299
  time to fit residues: 130.9554
Evaluate side-chains
  152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 106
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1372 ASP
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1410 LYS
Chi-restraints excluded: chain A residue 1476 ASP
Chi-restraints excluded: chain A residue 1518 VAL
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1567 PHE
Chi-restraints excluded: chain B residue 1372 ASP
Chi-restraints excluded: chain B residue 1410 LYS
Chi-restraints excluded: chain B residue 1520 VAL
Chi-restraints excluded: chain B residue 1524 ASP
Chi-restraints excluded: chain B residue 1613 LEU
Chi-restraints excluded: chain C residue 1372 ASP
Chi-restraints excluded: chain C residue 1380 ASP
Chi-restraints excluded: chain C residue 1397 LEU
Chi-restraints excluded: chain C residue 1452 ASN
Chi-restraints excluded: chain C residue 1520 VAL
Chi-restraints excluded: chain C residue 1557 GLU
Chi-restraints excluded: chain C residue 1605 GLU
Chi-restraints excluded: chain C residue 1613 LEU
Chi-restraints excluded: chain D residue 1372 ASP
Chi-restraints excluded: chain D residue 1398 VAL
Chi-restraints excluded: chain D residue 1404 THR
Chi-restraints excluded: chain D residue 1410 LYS
Chi-restraints excluded: chain D residue 1476 ASP
Chi-restraints excluded: chain D residue 1486 GLU
Chi-restraints excluded: chain D residue 1518 VAL
Chi-restraints excluded: chain D residue 1520 VAL
Chi-restraints excluded: chain D residue 1557 GLU
Chi-restraints excluded: chain D residue 1567 PHE
Chi-restraints excluded: chain E residue 1372 ASP
Chi-restraints excluded: chain E residue 1410 LYS
Chi-restraints excluded: chain E residue 1452 ASN
Chi-restraints excluded: chain E residue 1520 VAL
Chi-restraints excluded: chain E residue 1524 ASP
Chi-restraints excluded: chain E residue 1573 GLU
Chi-restraints excluded: chain E residue 1613 LEU
Chi-restraints excluded: chain F residue 1372 ASP
Chi-restraints excluded: chain F residue 1380 ASP
Chi-restraints excluded: chain F residue 1397 LEU
Chi-restraints excluded: chain F residue 1452 ASN
Chi-restraints excluded: chain F residue 1520 VAL
Chi-restraints excluded: chain F residue 1557 GLU
Chi-restraints excluded: chain F residue 1605 GLU
Chi-restraints excluded: chain F residue 1613 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 147 optimal weight:    8.9990
   chunk 112 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 133 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 127 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
A1452 ASN
B1594 ASN
C1452 ASN
E1594 ASN
F1452 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.139641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.125569 restraints weight = 18669.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.63
r_work: 0.3705 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.198  11640  Z= 0.266
  Angle     :  1.068  59.135  15948  Z= 0.660
  Chirality :  0.055   0.801   1884
  Planarity :  0.006   0.150   2130
  Dihedral  :  5.426  38.762   1578
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 21.31 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.64 (0.19), residues: 1506
  helix: -3.14 (0.39), residues: 72
  sheet:  0.18 (0.20), residues: 546
  loop : -1.82 (0.17), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1378 
 HIS   0.003   0.001   HIS F1391 
 PHE   0.016   0.003   PHE B1484 
 TYR   0.014   0.002   TYR D1383 
 ARG   0.005   0.001   ARG F1580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  378)
  hydrogen bonds       : angle       5.62556 ( 1278)
  covalent geometry    : bond        0.00544 (11640)
  covalent geometry    : angle       1.06838 (15948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8159.24 seconds
wall clock time: 141 minutes 14.53 seconds (8474.53 seconds total)