Starting phenix.real_space_refine
on Wed Mar  4 02:45:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qcl_13896/03_2026/7qcl_13896.map"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S     140      5.16       5
     C    6064      2.51       5
     N    1437      2.21       5
     O    2241      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9884
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 4177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 4177
          Classifications: {'peptide': 546}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 44, 'TRANS': 501}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 4177
          Classifications: {'peptide': 546}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 44, 'TRANS': 501}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "D"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 171
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 4, 'MAN': 2, 'NAG': 6}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 14
    Chain: "E"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "G"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "H"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 111
          Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    Chain: "I"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 60
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "J"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "K"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 111
          Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    Chain: "L"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "M"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "N"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 49
          Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "O"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 146
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 5}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 12
    Chain: "Q"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 121
          Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' CA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' CA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.03, per 1000 atoms: 0.21
  Number of scatterers: 9884
  At special positions: 0
  Unit cell: (128.14, 113.52, 197.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S     140     16.00
     O    2241      8.00
     N    1437      7.00
     C    6064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=60, symmetry=0
    Simple disulfide: pdb=" SG  CYS A4352 " - pdb=" SG  CYS A4386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4379 " - pdb=" SG  CYS B4379 " distance=2.29
    Simple disulfide: pdb=" SG  CYS A4381 " - pdb=" SG  CYS A4422 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A4399 " - pdb=" SG  CYS A4423 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A4407 " - pdb=" SG  CYS A4428 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A4430 " - pdb=" SG  CYS A4576 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A4432 " - pdb=" SG  CYS A4573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4454 " - pdb=" SG  CYS A4612 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4478 " - pdb=" SG  CYS A4486 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A4584 " - pdb=" SG  CYS A4595 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4638 " - pdb=" SG  CYS A4673 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4644 " - pdb=" SG  CYS A4668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4655 " - pdb=" SG  CYS A4692 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4682 " - pdb=" SG  CYS A4709 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A4698 " - pdb=" SG  CYS A4722 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4713 " - pdb=" SG  CYS A4746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4730 " - pdb=" SG  CYS A4766 " distance=2.18
    Simple disulfide: pdb=" SG  CYS A4748 " - pdb=" SG  CYS A4762 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4768 " - pdb=" SG  CYS A4791 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4786 " - pdb=" SG  CYS A4830 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A4789 " - pdb=" SG  CYS A4800 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4805 " - pdb=" SG  CYS A4831 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A4813 " - pdb=" SG  CYS A4836 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4838 " - pdb=" SG  CYS A4865 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A4843 " - pdb=" SG  CYS A4866 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4850 " - pdb=" SG  CYS A4871 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4877 " - pdb=" SG  CYS A4900 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4895 " - pdb=" SG  CYS A4937 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A4898 " - pdb=" SG  CYS A4915 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A4920 " - pdb=" SG  CYS A4938 " distance=2.09
    Simple disulfide: pdb=" SG  CYS A4924 " - pdb=" SG  CYS A4941 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B4352 " - pdb=" SG  CYS B4386 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B4381 " - pdb=" SG  CYS B4422 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B4399 " - pdb=" SG  CYS B4423 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B4407 " - pdb=" SG  CYS B4428 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4430 " - pdb=" SG  CYS B4576 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4432 " - pdb=" SG  CYS B4573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4454 " - pdb=" SG  CYS B4612 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4478 " - pdb=" SG  CYS B4486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4584 " - pdb=" SG  CYS B4595 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B4638 " - pdb=" SG  CYS B4673 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4644 " - pdb=" SG  CYS B4668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4655 " - pdb=" SG  CYS B4692 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4682 " - pdb=" SG  CYS B4709 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B4698 " - pdb=" SG  CYS B4722 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4713 " - pdb=" SG  CYS B4746 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B4730 " - pdb=" SG  CYS B4766 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B4748 " - pdb=" SG  CYS B4762 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4768 " - pdb=" SG  CYS B4791 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4786 " - pdb=" SG  CYS B4830 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4789 " - pdb=" SG  CYS B4800 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4805 " - pdb=" SG  CYS B4831 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B4813 " - pdb=" SG  CYS B4836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B4838 " - pdb=" SG  CYS B4865 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B4843 " - pdb=" SG  CYS B4866 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4850 " - pdb=" SG  CYS B4871 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4877 " - pdb=" SG  CYS B4900 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B4898 " - pdb=" SG  CYS B4915 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B4920 " - pdb=" SG  CYS B4938 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B4924 " - pdb=" SG  CYS B4941 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
      " NAG I   2 " - " MAN I   3 "
      " BMA J   3 " - " MAN J   4 "
      " BMA K   3 " - " MAN K   4 "
      " BMA L   3 " - " MAN L   4 "
      " BMA O   3 " - " MAN O   4 "
      " BMA Q   3 " - " MAN Q   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   7 "
      " BMA D   3 " - " MAN D   9 "
      " BMA F   3 " - " MAN F   7 "
      " BMA G   3 " - " MAN G   7 "
      " BMA H   3 " - " MAN H   7 "
      " BMA J   3 " - " MAN J   7 "
      " BMA K   3 " - " MAN K   7 "
      " BMA L   3 " - " MAN L   7 "
      " BMA O   3 " - " MAN O   9 "
      " BMA Q   3 " - " MAN Q   7 "
    BETA1-2
      " MAN C   4 " - " NAG C   5 "
      " MAN C   7 " - " NAG C   8 "
      " MAN D   4 " - " NAG D   5 "
      " MAN D   9 " - " NAG D  10 "
      " MAN F   4 " - " NAG F   5 "
      " MAN F   7 " - " NAG F   8 "
      " MAN G   4 " - " NAG G   5 "
      " MAN G   7 " - " NAG G   8 "
      " MAN H   4 " - " NAG H   5 "
      " MAN H   7 " - " NAG H   8 "
      " MAN J   4 " - " NAG J   5 "
      " MAN J   7 " - " NAG J   8 "
      " MAN K   4 " - " NAG K   5 "
      " MAN K   7 " - " NAG K   8 "
      " MAN L   4 " - " NAG L   5 "
      " MAN L   7 " - " NAG L   8 "
      " MAN O   4 " - " NAG O   5 "
      " MAN Q   4 " - " NAG Q   5 "
      " MAN Q   7 " - " NAG Q   8 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG C   5 " - " GAL C   6 "
      " NAG C   8 " - " GAL C   9 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " MAN D   4 " - " NAG D   7 "
      " NAG D   5 " - " GAL D   6 "
      " NAG D   7 " - " GAL D   8 "
      " MAN D   9 " - " NAG D  12 "
      " NAG D  10 " - " GAL D  11 "
      " NAG D  12 " - " GAL D  13 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG F   5 " - " GAL F   6 "
      " NAG F   8 " - " GAL F   9 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG G   5 " - " GAL G   6 "
      " NAG G   8 " - " GAL G   9 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG H   5 " - " GAL H   6 "
      " NAG H   8 " - " GAL H   9 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   4 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
      " NAG J   5 " - " GAL J   6 "
      " NAG J   8 " - " GAL J   9 "
      " NAG K   1 " - " NAG K   2 "
      " NAG K   2 " - " BMA K   3 "
      " NAG K   5 " - " GAL K   6 "
      " NAG K   8 " - " GAL K   9 "
      " NAG L   1 " - " NAG L   2 "
      " NAG L   2 " - " BMA L   3 "
      " NAG L   5 " - " GAL L   6 "
      " NAG L   8 " - " GAL L   9 "
      " NAG M   1 " - " NAG M   2 "
      " NAG M   2 " - " BMA M   3 "
      " NAG N   1 " - " NAG N   2 "
      " NAG N   2 " - " BMA N   3 "
      " NAG O   1 " - " NAG O   2 "
      " NAG O   2 " - " BMA O   3 "
      " MAN O   4 " - " NAG O   7 "
      " NAG O   5 " - " GAL O   6 "
      " NAG O   7 " - " GAL O   8 "
      " MAN O   9 " - " NAG O  10 "
      " NAG O  10 " - " GAL O  11 "
      " NAG Q   1 " - " NAG Q   2 "
      " NAG Q   2 " - " BMA Q   3 "
      " NAG Q   5 " - " GAL Q   6 "
      " NAG Q   8 " - " GAL Q   9 "
    BETA1-6
      " NAG C   1 " - " FUC C  10 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG D   1 " - " FUC D  14 "
      " NAG E   1 " - " FUC E   4 "
      " NAG F   1 " - " FUC F  10 "
      " NAG G   1 " - " FUC G  10 "
      " NAG I   1 " - " FUC I   5 "
      " NAG J   1 " - " FUC J  10 "
      " NAG L   1 " - " FUC L  10 "
      " NAG M   1 " - " FUC M   4 "
      " NAG N   1 " - " FUC N   4 "
      " NAG O   1 " - " FUC O  12 "
      " NAG Q   1 " - " FUC Q  10 "
    NAG-ASN
      " NAG A5002 " - " ASN A4389 "
      " NAG B5002 " - " ASN B4389 "
      " NAG C   1 " - " ASN A4832 "
      " NAG D   1 " - " ASN A4567 "
      " NAG E   1 " - " ASN B4906 "
      " NAG F   1 " - " ASN B4839 "
      " NAG G   1 " - " ASN A4703 "
      " NAG H   1 " - " ASN B4578 "
      " NAG I   1 " - " ASN A4738 "
      " NAG J   1 " - " ASN A4839 "
      " NAG K   1 " - " ASN A4578 "
      " NAG L   1 " - " ASN B4703 "
      " NAG M   1 " - " ASN A4906 "
      " NAG N   1 " - " ASN B4738 "
      " NAG O   1 " - " ASN B4567 "
      " NAG Q   1 " - " ASN B4832 "
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 427.1 milliseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 17 sheets defined
      11.3% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4579 through 4583
      removed outlier: 3.707A  pdb=" N   ASP A4582 " --> pdb=" O   THR A4579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4594 through 4600
      removed outlier: 3.558A  pdb=" N   ALA A4598 " --> pdb=" O   ASN A4594 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A4600 " --> pdb=" O   GLU A4596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4641 through 4646
    Processing helix  chain 'A' and resid 4647 through 4651
      removed outlier: 6.053A  pdb=" N   SER A4650 " --> pdb=" O   ILE A4647 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU A4651 " --> pdb=" O   LYS A4648 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4647 through 4651'
    Processing helix  chain 'A' and resid 4652 through 4657
      removed outlier: 4.140A  pdb=" N   ALA A4657 " --> pdb=" O   ALA A4653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4661 through 4675
      removed outlier: 3.732A  pdb=" N   MET A4675 " --> pdb=" O   ASP A4671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4683 through 4695
    Processing helix  chain 'A' and resid 4907 through 4912
    Processing helix  chain 'B' and resid 4594 through 4601
      removed outlier: 3.748A  pdb=" N   ALA B4598 " --> pdb=" O   ASN B4594 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B4599 " --> pdb=" O   CYS B4595 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ASP B4600 " --> pdb=" O   GLU B4596 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLN B4601 " --> pdb=" O   ALA B4597 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 4594 through 4601'
    Processing helix  chain 'B' and resid 4641 through 4646
      removed outlier: 3.789A  pdb=" N   GLN B4645 " --> pdb=" O   SER B4641 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B4646 " --> pdb=" O   PRO B4642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 4641 through 4646'
    Processing helix  chain 'B' and resid 4647 through 4648
      No H-bonds generated for 'chain 'B' and resid 4647 through 4648'
    Processing helix  chain 'B' and resid 4649 through 4653
      removed outlier: 3.563A  pdb=" N   PHE B4652 " --> pdb=" O   ASP B4649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4661 through 4675
      removed outlier: 3.721A  pdb=" N   MET B4675 " --> pdb=" O   ASP B4671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4683 through 4695
    Processing helix  chain 'B' and resid 4702 through 4706
      removed outlier: 3.535A  pdb=" N   HIS B4706 " --> pdb=" O   ASN B4703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4907 through 4912
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4382 through 4386
    Processing sheet with id=AA2, first strand: chain 'A' and resid 4414 through 4417
    Processing sheet with id=AA3, first strand: chain 'A' and resid 4430 through 4435
    Processing sheet with id=AA4, first strand: chain 'A' and resid 4439 through 4441
    Processing sheet with id=AA5, first strand: chain 'A' and resid 4509 through 4512
      removed outlier: 8.992A  pdb=" N   PHE A4469 " --> pdb=" O   GLU A4460 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   GLU A4460 " --> pdb=" O   PHE A4469 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL A4471 " --> pdb=" O   LEU A4458 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 4718 through 4723
      removed outlier: 4.363A  pdb=" N   CYS A4722 " --> pdb=" O   VAL A4743 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   VAL A4743 " --> pdb=" O   CYS A4722 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 4753 through 4754
    Processing sheet with id=AA8, first strand: chain 'A' and resid 4780 through 4782
      removed outlier: 3.695A  pdb=" N   GLU A4780 " --> pdb=" O   CYS A4791 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS A4789 " --> pdb=" O   PHE A4782 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 4823 through 4824
    Processing sheet with id=AB1, first strand: chain 'B' and resid 4414 through 4417
    Processing sheet with id=AB2, first strand: chain 'B' and resid 4447 through 4449
    Processing sheet with id=AB3, first strand: chain 'B' and resid 4509 through 4512
      removed outlier: 6.662A  pdb=" N   VAL B4471 " --> pdb=" O   LEU B4458 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS B4570 " --> pdb=" O   GLU B4460 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 4718 through 4723
      removed outlier: 4.534A  pdb=" N   CYS B4722 " --> pdb=" O   VAL B4743 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL B4743 " --> pdb=" O   CYS B4722 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 4753 through 4754
    Processing sheet with id=AB6, first strand: chain 'B' and resid 4768 through 4769
    Processing sheet with id=AB7, first strand: chain 'B' and resid 4780 through 4782
    Processing sheet with id=AB8, first strand: chain 'B' and resid 4818 through 4822

    198 hydrogen bonds defined for protein.
    501 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: 1.34

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1503
        1.31 -     1.44: 2942
        1.44 -     1.56: 5501
        1.56 -     1.69: 4
        1.69 -     1.82: 158
  Bond restraints: 10108
  Sorted by residual:
  bond pdb=" CA  VAL B4861 "
       pdb=" C   VAL B4861 "
    ideal  model  delta    sigma   weight residual
    1.524  1.595 -0.070 1.05e-02 9.07e+03 4.47e+01
  bond pdb=" N   CYS A4399 "
       pdb=" CA  CYS A4399 "
    ideal  model  delta    sigma   weight residual
    1.458  1.511 -0.054 1.18e-02 7.18e+03 2.09e+01
  bond pdb=" CA  VAL A4814 "
       pdb=" C   VAL A4814 "
    ideal  model  delta    sigma   weight residual
    1.519  1.569 -0.050 1.14e-02 7.69e+03 1.94e+01
  bond pdb=" CA  SER B4873 "
       pdb=" CB  SER B4873 "
    ideal  model  delta    sigma   weight residual
    1.528  1.464  0.064 1.48e-02 4.57e+03 1.87e+01
  bond pdb=" C   MET B4383 "
       pdb=" O   MET B4383 "
    ideal  model  delta    sigma   weight residual
    1.234  1.177  0.057 1.38e-02 5.25e+03 1.72e+01
  ... (remaining 10103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 12852
        3.37 -     6.74: 820
        6.74 -    10.11: 100
       10.11 -    13.48: 17
       13.48 -    16.85: 4
  Bond angle restraints: 13793
  Sorted by residual:
  angle pdb=" N   GLY A4927 "
        pdb=" CA  GLY A4927 "
        pdb=" C   GLY A4927 "
      ideal   model   delta    sigma   weight residual
     113.58  100.81   12.77 1.07e+00 8.73e-01 1.42e+02
  angle pdb=" N   VAL A4904 "
        pdb=" CA  VAL A4904 "
        pdb=" C   VAL A4904 "
      ideal   model   delta    sigma   weight residual
     110.74  120.37   -9.63 9.10e-01 1.21e+00 1.12e+02
  angle pdb=" N   ASN B4825 "
        pdb=" CA  ASN B4825 "
        pdb=" C   ASN B4825 "
      ideal   model   delta    sigma   weight residual
     109.42   94.11   15.31 1.48e+00 4.57e-01 1.07e+02
  angle pdb=" N   VAL A4904 "
        pdb=" CA  VAL A4904 "
        pdb=" CB  VAL A4904 "
      ideal   model   delta    sigma   weight residual
     110.64   98.46   12.18 1.20e+00 6.94e-01 1.03e+02
  angle pdb=" N   LYS B4844 "
        pdb=" CA  LYS B4844 "
        pdb=" C   LYS B4844 "
      ideal   model   delta    sigma   weight residual
     111.36  122.14  -10.78 1.09e+00 8.42e-01 9.78e+01
  ... (remaining 13788 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.98: 6988
       23.98 -    47.97: 446
       47.97 -    71.95: 82
       71.95 -    95.93: 90
       95.93 -   119.92: 189
  Dihedral angle restraints: 7795
    sinusoidal: 4619
      harmonic: 3176
  Sorted by residual:
  dihedral pdb=" CB  CYS A4682 "
           pdb=" SG  CYS A4682 "
           pdb=" SG  CYS A4709 "
           pdb=" CB  CYS A4709 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.06  -89.94     1      1.00e+01 1.00e-02 9.59e+01
  dihedral pdb=" CB  CYS B4713 "
           pdb=" SG  CYS B4713 "
           pdb=" SG  CYS B4746 "
           pdb=" CB  CYS B4746 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.83  -86.83     1      1.00e+01 1.00e-02 9.07e+01
  dihedral pdb=" CB  CYS A4399 "
           pdb=" SG  CYS A4399 "
           pdb=" SG  CYS A4423 "
           pdb=" CB  CYS A4423 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.39   86.39     1      1.00e+01 1.00e-02 9.00e+01
  ... (remaining 7792 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.198: 1727
       0.198 -    0.396: 146
       0.396 -    0.594: 17
       0.594 -    0.791: 3
       0.791 -    0.989: 4
  Chirality restraints: 1897
  Sorted by residual:
  chirality pdb=" C1  NAG D   5 "
            pdb=" O2  MAN D   4 "
            pdb=" C2  NAG D   5 "
            pdb=" O5  NAG D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.41   -0.99 2.00e-02 2.50e+03 2.45e+03
  chirality pdb=" C1  NAG L   5 "
            pdb=" O2  MAN L   4 "
            pdb=" C2  NAG L   5 "
            pdb=" O5  NAG L   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.43   -0.97 2.00e-02 2.50e+03 2.35e+03
  chirality pdb=" C1  MAN L   4 "
            pdb=" O3  BMA L   3 "
            pdb=" C2  MAN L   4 "
            pdb=" O5  MAN L   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.56    0.84 2.00e-02 2.50e+03 1.74e+03
  ... (remaining 1894 not shown)

  Planarity restraints: 1621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG I   1 "   -0.355 2.00e-02 2.50e+03   3.05e-01 1.16e+03
        pdb=" C7  NAG I   1 "    0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG I   1 "   -0.131 2.00e-02 2.50e+03
        pdb=" N2  NAG I   1 "    0.543 2.00e-02 2.50e+03
        pdb=" O7  NAG I   1 "   -0.143 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG Q   5 "   -0.355 2.00e-02 2.50e+03   3.05e-01 1.16e+03
        pdb=" C7  NAG Q   5 "    0.087 2.00e-02 2.50e+03
        pdb=" C8  NAG Q   5 "   -0.142 2.00e-02 2.50e+03
        pdb=" N2  NAG Q   5 "    0.542 2.00e-02 2.50e+03
        pdb=" O7  NAG Q   5 "   -0.131 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG I   2 "    0.353 2.00e-02 2.50e+03   3.03e-01 1.15e+03
        pdb=" C7  NAG I   2 "   -0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG I   2 "    0.145 2.00e-02 2.50e+03
        pdb=" N2  NAG I   2 "   -0.539 2.00e-02 2.50e+03
        pdb=" O7  NAG I   2 "    0.127 2.00e-02 2.50e+03
  ... (remaining 1618 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.43: 45
        2.43 -     3.05: 7471
        3.05 -     3.67: 15040
        3.67 -     4.28: 22328
        4.28 -     4.90: 33440
  Nonbonded interactions: 78324
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A4398 "
            pdb=" O   CYS A4399 "
     model   vdw
     1.816 3.040
  nonbonded pdb=" OG1 THR A4577 "
            pdb="CA    CA A5003 "
     model   vdw
     1.864 2.510
  nonbonded pdb=" CE3 TRP A4376 "
            pdb=" O   TRP A4377 "
     model   vdw
     1.871 3.340
  nonbonded pdb=" ND1 HIS A4505 "
            pdb=" CE  MET A4506 "
     model   vdw
     2.001 3.540
  nonbonded pdb=" OD1 ASP A4583 "
            pdb="CA    CA A5003 "
     model   vdw
     2.040 2.510
  ... (remaining 78319 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 2)
  selection = (chain 'F' and resid 2)
  selection = (chain 'G' and resid 2)
  selection = (chain 'H' and resid 1)
  selection = (chain 'J' and resid 2)
  selection = (chain 'K' and resid 1)
  selection = (chain 'L' and resid 2)
  selection = (chain 'Q' and resid 2)
}
ncs_group {
  reference = (chain 'D' and (resid 7 through 8 or resid 12 through 14))
  selection = (chain 'O' and (resid 5 through 6 or resid 10 through 12))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'M'
  selection = chain 'N'
}

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:             17.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.960
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5477
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      :  0.011   0.256  10291  Z= 0.714
  Angle     :  1.958  48.427  14282  Z= 1.156
  Chirality :  0.123   0.989   1897
  Planarity :  0.038   0.305   1605
  Dihedral  : 25.313 119.917   5571
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 36.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.94 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  :  6.66 %
    Favored  : 86.68 %
  Cbeta Deviations :  2.64 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.25), residues: 1076
  helix:  1.36 (0.65), residues: 74
  sheet: -0.01 (0.37), residues: 204
  loop : -2.01 (0.21), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B4804 
 TYR   0.016   0.001   TYR A4869 
 PHE   0.018   0.002   PHE A4928 
 TRP   0.024   0.003   TRP A4424 
 HIS   0.013   0.001   HIS A4425 

Details of bonding type rmsd
  covalent geometry    : bond        0.01061 (10108)
  covalent geometry    : angle       1.77778 (13793)
  SS BOND              : bond        0.04076 (   60)
  SS BOND              : angle       5.45110 (  120)
  hydrogen bonds       : bond        0.17228 (  198)
  hydrogen bonds       : angle       8.39968 (  501)
  link_ALPHA1-3        : bond        0.00478 (   11)
  link_ALPHA1-3        : angle       3.11335 (   33)
  link_ALPHA1-6        : bond        0.00658 (   10)
  link_ALPHA1-6        : angle       2.71753 (   30)
  link_BETA1-2         : bond        0.00497 (   19)
  link_BETA1-2         : angle       2.89439 (   57)
  link_BETA1-4         : bond        0.00532 (   55)
  link_BETA1-4         : angle       2.43408 (  165)
  link_BETA1-6         : bond        0.00317 (   12)
  link_BETA1-6         : angle       1.84587 (   36)
  link_NAG-ASN         : bond        0.02441 (   16)
  link_NAG-ASN         : angle      10.70748 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 67
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4703 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6707 (t0)
REVERT: A 4892 SER cc_start: 0.4851 (OUTLIER) cc_final: 0.4554 (t)
  outliers start: 65
  outliers final: 26
  residues processed: 127
  average time/residue: 0.0817
  time to fit residues: 15.1096
Evaluate side-chains
  70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 42
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4579 THR
Chi-restraints excluded: chain A residue 4595 CYS
Chi-restraints excluded: chain A residue 4703 ASN
Chi-restraints excluded: chain A residue 4734 SER
Chi-restraints excluded: chain A residue 4813 CYS
Chi-restraints excluded: chain A residue 4846 LYS
Chi-restraints excluded: chain A residue 4866 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4892 SER
Chi-restraints excluded: chain A residue 4908 THR
Chi-restraints excluded: chain A residue 4912 VAL
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain B residue 4351 GLU
Chi-restraints excluded: chain B residue 4352 CYS
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4478 CYS
Chi-restraints excluded: chain B residue 4730 CYS
Chi-restraints excluded: chain B residue 4815 GLU
Chi-restraints excluded: chain B residue 4837 LYS
Chi-restraints excluded: chain B residue 4840 THR
Chi-restraints excluded: chain B residue 4859 LYS
Chi-restraints excluded: chain B residue 4860 MET
Chi-restraints excluded: chain B residue 4865 CYS
Chi-restraints excluded: chain B residue 4866 CYS
Chi-restraints excluded: chain B residue 4900 CYS
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4924 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A4917 HIS
** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4645 GLN
** B4739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.104317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.072851 restraints weight = 43491.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 5.74
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099  10291  Z= 0.274
  Angle     :  1.360  29.089  14282  Z= 0.559
  Chirality :  0.067   0.553   1897
  Planarity :  0.006   0.063   1605
  Dihedral  : 23.053 117.012   3661
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 11.27 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.25), residues: 1076
  helix:  1.98 (0.67), residues: 74
  sheet:  0.16 (0.35), residues: 212
  loop : -1.95 (0.22), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A4864 
 TYR   0.032   0.002   TYR B4476 
 PHE   0.021   0.002   PHE A4854 
 TRP   0.030   0.002   TRP A4376 
 HIS   0.006   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (10108)
  covalent geometry    : angle       1.25558 (13793)
  SS BOND              : bond        0.00477 (   60)
  SS BOND              : angle       2.04461 (  120)
  hydrogen bonds       : bond        0.04164 (  198)
  hydrogen bonds       : angle       7.30803 (  501)
  link_ALPHA1-3        : bond        0.01738 (   11)
  link_ALPHA1-3        : angle       3.54947 (   33)
  link_ALPHA1-6        : bond        0.01260 (   10)
  link_ALPHA1-6        : angle       2.58987 (   30)
  link_BETA1-2         : bond        0.01177 (   19)
  link_BETA1-2         : angle       1.94846 (   57)
  link_BETA1-4         : bond        0.01116 (   55)
  link_BETA1-4         : angle       2.96694 (  165)
  link_BETA1-6         : bond        0.00863 (   12)
  link_BETA1-6         : angle       1.75654 (   36)
  link_NAG-ASN         : bond        0.01873 (   16)
  link_NAG-ASN         : angle       6.04623 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 46
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4376 TRP cc_start: 0.8800 (t60) cc_final: 0.8421 (t60)
REVERT: A 4852 LEU cc_start: 0.8210 (mt) cc_final: 0.7968 (mt)
REVERT: A 4916 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (p)
REVERT: A 4924 CYS cc_start: 0.5010 (OUTLIER) cc_final: 0.4545 (m)
REVERT: B 4406 THR cc_start: 0.8879 (m) cc_final: 0.8664 (p)
  outliers start: 36
  outliers final: 24
  residues processed: 79
  average time/residue: 0.0785
  time to fit residues: 9.4801
Evaluate side-chains
  69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4579 THR
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4908 THR
Chi-restraints excluded: chain A residue 4912 VAL
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4924 CYS
Chi-restraints excluded: chain A residue 4941 CYS
Chi-restraints excluded: chain B residue 4351 GLU
Chi-restraints excluded: chain B residue 4352 CYS
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4584 CYS
Chi-restraints excluded: chain B residue 4730 CYS
Chi-restraints excluded: chain B residue 4840 THR
Chi-restraints excluded: chain B residue 4859 LYS
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4900 CYS
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Chi-restraints excluded: chain B residue 4941 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B4512 GLN
B4552 ASN
B4686 GLN
B4739 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.104978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.073251 restraints weight = 43012.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 5.75
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090  10291  Z= 0.213
  Angle     :  1.139  29.050  14282  Z= 0.467
  Chirality :  0.058   0.508   1897
  Planarity :  0.005   0.050   1605
  Dihedral  : 19.729 114.965   3636
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.11 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.63 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.26), residues: 1076
  helix:  1.96 (0.65), residues: 77
  sheet:  0.42 (0.35), residues: 206
  loop : -1.87 (0.22), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B4804 
 TYR   0.022   0.001   TYR A4891 
 PHE   0.017   0.001   PHE B4928 
 TRP   0.029   0.002   TRP A4870 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (10108)
  covalent geometry    : angle       1.04769 (13793)
  SS BOND              : bond        0.00582 (   60)
  SS BOND              : angle       1.61915 (  120)
  hydrogen bonds       : bond        0.03518 (  198)
  hydrogen bonds       : angle       6.92441 (  501)
  link_ALPHA1-3        : bond        0.01417 (   11)
  link_ALPHA1-3        : angle       2.88377 (   33)
  link_ALPHA1-6        : bond        0.01221 (   10)
  link_ALPHA1-6        : angle       2.58588 (   30)
  link_BETA1-2         : bond        0.00935 (   19)
  link_BETA1-2         : angle       1.72219 (   57)
  link_BETA1-4         : bond        0.00967 (   55)
  link_BETA1-4         : angle       2.70342 (  165)
  link_BETA1-6         : bond        0.00722 (   12)
  link_BETA1-6         : angle       1.74644 (   36)
  link_NAG-ASN         : bond        0.00836 (   16)
  link_NAG-ASN         : angle       4.78856 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 49
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4675 MET cc_start: 0.8856 (ptp) cc_final: 0.8617 (ptp)
REVERT: A 4852 LEU cc_start: 0.8150 (mt) cc_final: 0.7670 (tp)
REVERT: A 4929 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6127 (tp30)
  outliers start: 36
  outliers final: 26
  residues processed: 82
  average time/residue: 0.0725
  time to fit residues: 9.2563
Evaluate side-chains
  64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 38
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4579 THR
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4908 THR
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4916 THR
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain A residue 4941 CYS
Chi-restraints excluded: chain B residue 4351 GLU
Chi-restraints excluded: chain B residue 4388 TYR
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4584 CYS
Chi-restraints excluded: chain B residue 4730 CYS
Chi-restraints excluded: chain B residue 4859 LYS
Chi-restraints excluded: chain B residue 4869 TYR
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0030
   chunk 45 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4552 ASN
B4686 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.105166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.073359 restraints weight = 43755.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 5.73
r_work: 0.3039 rms_B_bonded: 5.68 restraints_weight: 2.0000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  10291  Z= 0.184
  Angle     :  1.077  29.094  14282  Z= 0.438
  Chirality :  0.056   0.457   1897
  Planarity :  0.005   0.046   1605
  Dihedral  : 18.320 111.614   3632
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.45 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.25), residues: 1076
  helix:  1.90 (0.65), residues: 77
  sheet:  0.43 (0.36), residues: 203
  loop : -1.94 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B4804 
 TYR   0.019   0.001   TYR A4869 
 PHE   0.026   0.001   PHE A4854 
 TRP   0.034   0.002   TRP B4870 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10108)
  covalent geometry    : angle       0.98793 (13793)
  SS BOND              : bond        0.00518 (   60)
  SS BOND              : angle       1.33659 (  120)
  hydrogen bonds       : bond        0.03011 (  198)
  hydrogen bonds       : angle       6.61120 (  501)
  link_ALPHA1-3        : bond        0.01468 (   11)
  link_ALPHA1-3        : angle       2.78775 (   33)
  link_ALPHA1-6        : bond        0.01249 (   10)
  link_ALPHA1-6        : angle       2.38928 (   30)
  link_BETA1-2         : bond        0.01001 (   19)
  link_BETA1-2         : angle       1.79342 (   57)
  link_BETA1-4         : bond        0.00920 (   55)
  link_BETA1-4         : angle       2.73117 (  165)
  link_BETA1-6         : bond        0.00716 (   12)
  link_BETA1-6         : angle       1.63099 (   36)
  link_NAG-ASN         : bond        0.01094 (   16)
  link_NAG-ASN         : angle       4.47548 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 44
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4852 LEU cc_start: 0.8193 (mt) cc_final: 0.7713 (tp)
REVERT: A 4929 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6101 (mm-30)
REVERT: B 4870 TRP cc_start: 0.8151 (p-90) cc_final: 0.7855 (p-90)
  outliers start: 30
  outliers final: 20
  residues processed: 70
  average time/residue: 0.0790
  time to fit residues: 8.6147
Evaluate side-chains
  60 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4395 VAL
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4753 MET
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4406 THR
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4584 CYS
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4859 LYS
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B4552 ASN
B4686 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.099673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.066118 restraints weight = 44541.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 5.05
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  10291  Z= 0.208
  Angle     :  1.048  24.160  14282  Z= 0.430
  Chirality :  0.055   0.458   1897
  Planarity :  0.005   0.053   1605
  Dihedral  : 17.245 112.947   3625
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.57 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.25), residues: 1076
  helix:  2.17 (0.68), residues: 71
  sheet:  0.61 (0.36), residues: 201
  loop : -1.83 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B4804 
 TYR   0.014   0.001   TYR B4891 
 PHE   0.015   0.001   PHE B4854 
 TRP   0.033   0.003   TRP B4377 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (10108)
  covalent geometry    : angle       0.95997 (13793)
  SS BOND              : bond        0.00524 (   60)
  SS BOND              : angle       1.33994 (  120)
  hydrogen bonds       : bond        0.03509 (  198)
  hydrogen bonds       : angle       6.52188 (  501)
  link_ALPHA1-3        : bond        0.01336 (   11)
  link_ALPHA1-3        : angle       2.68809 (   33)
  link_ALPHA1-6        : bond        0.01238 (   10)
  link_ALPHA1-6        : angle       2.31015 (   30)
  link_BETA1-2         : bond        0.00893 (   19)
  link_BETA1-2         : angle       1.72764 (   57)
  link_BETA1-4         : bond        0.00850 (   55)
  link_BETA1-4         : angle       2.70618 (  165)
  link_BETA1-6         : bond        0.00675 (   12)
  link_BETA1-6         : angle       1.70240 (   36)
  link_NAG-ASN         : bond        0.00990 (   16)
  link_NAG-ASN         : angle       4.24680 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 43
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4760 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7749 (t0)
REVERT: A 4852 LEU cc_start: 0.8250 (mt) cc_final: 0.7835 (tp)
REVERT: B 4870 TRP cc_start: 0.7802 (p-90) cc_final: 0.7594 (p-90)
  outliers start: 30
  outliers final: 23
  residues processed: 70
  average time/residue: 0.0720
  time to fit residues: 7.7217
Evaluate side-chains
  61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4459 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4753 MET
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4406 THR
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4584 CYS
Chi-restraints excluded: chain B residue 4790 VAL
Chi-restraints excluded: chain B residue 4840 THR
Chi-restraints excluded: chain B residue 4859 LYS
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 76 optimal weight:    0.1980
   chunk 85 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 106 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B4552 ASN
B4686 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.100231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.066904 restraints weight = 44117.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 4.97
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10291  Z= 0.174
  Angle     :  1.011  21.812  14282  Z= 0.415
  Chirality :  0.054   0.424   1897
  Planarity :  0.005   0.067   1605
  Dihedral  : 16.470 112.788   3625
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.09 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.25), residues: 1076
  helix:  1.83 (0.65), residues: 77
  sheet:  0.83 (0.36), residues: 193
  loop : -1.82 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A4804 
 TYR   0.016   0.001   TYR A4884 
 PHE   0.012   0.001   PHE A4854 
 TRP   0.025   0.002   TRP A4870 
 HIS   0.005   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10108)
  covalent geometry    : angle       0.92601 (13793)
  SS BOND              : bond        0.00377 (   60)
  SS BOND              : angle       1.17302 (  120)
  hydrogen bonds       : bond        0.02965 (  198)
  hydrogen bonds       : angle       6.32260 (  501)
  link_ALPHA1-3        : bond        0.01364 (   11)
  link_ALPHA1-3        : angle       2.58523 (   33)
  link_ALPHA1-6        : bond        0.01248 (   10)
  link_ALPHA1-6        : angle       2.21370 (   30)
  link_BETA1-2         : bond        0.00925 (   19)
  link_BETA1-2         : angle       1.74193 (   57)
  link_BETA1-4         : bond        0.00844 (   55)
  link_BETA1-4         : angle       2.64972 (  165)
  link_BETA1-6         : bond        0.00688 (   12)
  link_BETA1-6         : angle       1.60443 (   36)
  link_NAG-ASN         : bond        0.00948 (   16)
  link_NAG-ASN         : angle       4.12667 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 42
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4760 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7745 (t0)
REVERT: A 4792 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8561 (pp)
REVERT: A 4852 LEU cc_start: 0.8243 (mt) cc_final: 0.7796 (tp)
REVERT: A 4860 MET cc_start: 0.6315 (mmp) cc_final: 0.6055 (mmm)
  outliers start: 33
  outliers final: 19
  residues processed: 71
  average time/residue: 0.0745
  time to fit residues: 8.0374
Evaluate side-chains
  60 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4792 LEU
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4840 THR
Chi-restraints excluded: chain B residue 4869 TYR
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0070
   chunk 69 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A4881 ASN
B4552 ASN
B4686 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.105166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.072395 restraints weight = 43467.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 5.44
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10291  Z= 0.174
  Angle     :  0.993  21.532  14282  Z= 0.408
  Chirality :  0.053   0.414   1897
  Planarity :  0.004   0.044   1605
  Dihedral  : 15.883 113.627   3621
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.11 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.25), residues: 1076
  helix:  2.13 (0.67), residues: 71
  sheet:  1.01 (0.36), residues: 187
  loop : -1.77 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A4804 
 TYR   0.014   0.001   TYR A4884 
 PHE   0.009   0.001   PHE A4854 
 TRP   0.032   0.002   TRP B4870 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10108)
  covalent geometry    : angle       0.90851 (13793)
  SS BOND              : bond        0.00382 (   60)
  SS BOND              : angle       1.20625 (  120)
  hydrogen bonds       : bond        0.03047 (  198)
  hydrogen bonds       : angle       6.21827 (  501)
  link_ALPHA1-3        : bond        0.01316 (   11)
  link_ALPHA1-3        : angle       2.55781 (   33)
  link_ALPHA1-6        : bond        0.01207 (   10)
  link_ALPHA1-6        : angle       2.18469 (   30)
  link_BETA1-2         : bond        0.00874 (   19)
  link_BETA1-2         : angle       1.71801 (   57)
  link_BETA1-4         : bond        0.00811 (   55)
  link_BETA1-4         : angle       2.60976 (  165)
  link_BETA1-6         : bond        0.00667 (   12)
  link_BETA1-6         : angle       1.63709 (   36)
  link_NAG-ASN         : bond        0.00911 (   16)
  link_NAG-ASN         : angle       4.03936 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 41
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4760 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7761 (t0)
REVERT: A 4792 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8678 (pp)
REVERT: A 4852 LEU cc_start: 0.8268 (mt) cc_final: 0.7846 (tp)
REVERT: A 4931 MET cc_start: 0.5993 (mmp) cc_final: 0.3616 (tmm)
REVERT: B 4375 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8592 (p)
REVERT: B 4816 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8707 (p0)
  outliers start: 29
  outliers final: 22
  residues processed: 68
  average time/residue: 0.0663
  time to fit residues: 7.2750
Evaluate side-chains
  64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 38
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4459 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4792 LEU
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4375 THR
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4406 THR
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4774 VAL
Chi-restraints excluded: chain B residue 4790 VAL
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4816 ASP
Chi-restraints excluded: chain B residue 4866 CYS
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Chi-restraints excluded: chain B residue 4940 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0770
   chunk 99 optimal weight:    0.3980
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B4552 ASN
** B4885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.105705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.072976 restraints weight = 43482.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 5.48
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10291  Z= 0.171
  Angle     :  0.985  20.742  14282  Z= 0.404
  Chirality :  0.053   0.413   1897
  Planarity :  0.004   0.039   1605
  Dihedral  : 15.428 113.892   3621
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.73 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.25), residues: 1076
  helix:  1.96 (0.67), residues: 73
  sheet:  0.72 (0.36), residues: 200
  loop : -1.77 (0.21), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4804 
 TYR   0.015   0.001   TYR A4884 
 PHE   0.009   0.001   PHE A4854 
 TRP   0.028   0.002   TRP B4376 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10108)
  covalent geometry    : angle       0.90161 (13793)
  SS BOND              : bond        0.00354 (   60)
  SS BOND              : angle       1.16883 (  120)
  hydrogen bonds       : bond        0.02972 (  198)
  hydrogen bonds       : angle       6.18392 (  501)
  link_ALPHA1-3        : bond        0.01295 (   11)
  link_ALPHA1-3        : angle       2.51313 (   33)
  link_ALPHA1-6        : bond        0.01191 (   10)
  link_ALPHA1-6        : angle       2.15230 (   30)
  link_BETA1-2         : bond        0.00871 (   19)
  link_BETA1-2         : angle       1.72478 (   57)
  link_BETA1-4         : bond        0.00803 (   55)
  link_BETA1-4         : angle       2.56675 (  165)
  link_BETA1-6         : bond        0.00677 (   12)
  link_BETA1-6         : angle       1.62972 (   36)
  link_NAG-ASN         : bond        0.00897 (   16)
  link_NAG-ASN         : angle       3.99958 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 40
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4760 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7884 (t0)
REVERT: A 4792 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: A 4852 LEU cc_start: 0.8294 (mt) cc_final: 0.7855 (tp)
REVERT: A 4931 MET cc_start: 0.6051 (mmp) cc_final: 0.3666 (tmm)
REVERT: B 4404 MET cc_start: 0.8747 (tpp) cc_final: 0.8490 (tpt)
REVERT: B 4816 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8703 (p0)
  outliers start: 26
  outliers final: 21
  residues processed: 63
  average time/residue: 0.0647
  time to fit residues: 6.5253
Evaluate side-chains
  59 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4388 TYR
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4459 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4792 LEU
Chi-restraints excluded: chain A residue 4850 CYS
Chi-restraints excluded: chain A residue 4877 CYS
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4915 CYS
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4406 THR
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4774 VAL
Chi-restraints excluded: chain B residue 4790 VAL
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4816 ASP
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 18 optimal weight:    0.2980
   chunk 84 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 93 optimal weight:    0.3980
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.106013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.073312 restraints weight = 43575.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 5.59
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10291  Z= 0.161
  Angle     :  0.970  19.728  14282  Z= 0.401
  Chirality :  0.053   0.418   1897
  Planarity :  0.004   0.040   1605
  Dihedral  : 14.989 114.092   3621
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.42 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.26), residues: 1076
  helix:  1.94 (0.67), residues: 73
  sheet:  0.83 (0.36), residues: 194
  loop : -1.73 (0.22), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4804 
 TYR   0.013   0.001   TYR A4884 
 PHE   0.028   0.001   PHE A4854 
 TRP   0.032   0.002   TRP B4376 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10108)
  covalent geometry    : angle       0.89051 (13793)
  SS BOND              : bond        0.00343 (   60)
  SS BOND              : angle       1.12709 (  120)
  hydrogen bonds       : bond        0.02812 (  198)
  hydrogen bonds       : angle       6.09593 (  501)
  link_ALPHA1-3        : bond        0.01286 (   11)
  link_ALPHA1-3        : angle       2.46336 (   33)
  link_ALPHA1-6        : bond        0.01177 (   10)
  link_ALPHA1-6        : angle       2.09435 (   30)
  link_BETA1-2         : bond        0.00858 (   19)
  link_BETA1-2         : angle       1.70835 (   57)
  link_BETA1-4         : bond        0.00799 (   55)
  link_BETA1-4         : angle       2.49319 (  165)
  link_BETA1-6         : bond        0.00687 (   12)
  link_BETA1-6         : angle       1.61207 (   36)
  link_NAG-ASN         : bond        0.00892 (   16)
  link_NAG-ASN         : angle       3.91702 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 39
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4675 MET cc_start: 0.8840 (ptp) cc_final: 0.8232 (mpp)
REVERT: A 4760 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7874 (t0)
REVERT: A 4792 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8549 (pp)
REVERT: A 4852 LEU cc_start: 0.8254 (mt) cc_final: 0.7814 (tp)
REVERT: A 4931 MET cc_start: 0.6083 (mmp) cc_final: 0.3768 (tmm)
REVERT: B 4404 MET cc_start: 0.8676 (tpp) cc_final: 0.8403 (tpp)
REVERT: B 4816 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8775 (p0)
  outliers start: 27
  outliers final: 20
  residues processed: 62
  average time/residue: 0.0614
  time to fit residues: 6.1785
Evaluate side-chains
  60 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 37
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4459 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4792 LEU
Chi-restraints excluded: chain A residue 4891 TYR
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4397 VAL
Chi-restraints excluded: chain B residue 4406 THR
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4774 VAL
Chi-restraints excluded: chain B residue 4790 VAL
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4816 ASP
Chi-restraints excluded: chain B residue 4866 CYS
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.1980
   chunk 104 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.4438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.106346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.073743 restraints weight = 43327.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 5.57
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  10291  Z= 0.159
  Angle     :  0.970  18.906  14282  Z= 0.399
  Chirality :  0.052   0.429   1897
  Planarity :  0.004   0.041   1605
  Dihedral  : 14.510 113.754   3620
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.73 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.26), residues: 1076
  helix:  2.09 (0.67), residues: 72
  sheet:  0.61 (0.36), residues: 202
  loop : -1.71 (0.22), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4804 
 TYR   0.015   0.001   TYR A4884 
 PHE   0.031   0.001   PHE A4854 
 TRP   0.046   0.002   TRP B4376 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10108)
  covalent geometry    : angle       0.89392 (13793)
  SS BOND              : bond        0.00447 (   60)
  SS BOND              : angle       1.14403 (  120)
  hydrogen bonds       : bond        0.02748 (  198)
  hydrogen bonds       : angle       6.02711 (  501)
  link_ALPHA1-3        : bond        0.01266 (   11)
  link_ALPHA1-3        : angle       2.41944 (   33)
  link_ALPHA1-6        : bond        0.01158 (   10)
  link_ALPHA1-6        : angle       2.05218 (   30)
  link_BETA1-2         : bond        0.00852 (   19)
  link_BETA1-2         : angle       1.69665 (   57)
  link_BETA1-4         : bond        0.00791 (   55)
  link_BETA1-4         : angle       2.43490 (  165)
  link_BETA1-6         : bond        0.00719 (   12)
  link_BETA1-6         : angle       1.61564 (   36)
  link_NAG-ASN         : bond        0.00887 (   16)
  link_NAG-ASN         : angle       3.85110 (   48)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 40
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4675 MET cc_start: 0.8823 (ptp) cc_final: 0.8228 (mpp)
REVERT: A 4760 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7860 (t0)
REVERT: A 4792 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8533 (pp)
REVERT: A 4852 LEU cc_start: 0.8197 (mt) cc_final: 0.7738 (tp)
REVERT: B 4404 MET cc_start: 0.8600 (tpp) cc_final: 0.8306 (tpp)
REVERT: B 4816 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8770 (p0)
  outliers start: 25
  outliers final: 18
  residues processed: 62
  average time/residue: 0.0734
  time to fit residues: 7.2002
Evaluate side-chains
  57 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 36
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4457 VAL
Chi-restraints excluded: chain A residue 4459 VAL
Chi-restraints excluded: chain A residue 4500 LEU
Chi-restraints excluded: chain A residue 4760 ASP
Chi-restraints excluded: chain A residue 4792 LEU
Chi-restraints excluded: chain A residue 4891 TYR
Chi-restraints excluded: chain A residue 4906 ASN
Chi-restraints excluded: chain A residue 4913 ILE
Chi-restraints excluded: chain A residue 4928 PHE
Chi-restraints excluded: chain B residue 4392 VAL
Chi-restraints excluded: chain B residue 4397 VAL
Chi-restraints excluded: chain B residue 4457 VAL
Chi-restraints excluded: chain B residue 4522 LEU
Chi-restraints excluded: chain B residue 4774 VAL
Chi-restraints excluded: chain B residue 4790 VAL
Chi-restraints excluded: chain B residue 4814 VAL
Chi-restraints excluded: chain B residue 4816 ASP
Chi-restraints excluded: chain B residue 4878 VAL
Chi-restraints excluded: chain B residue 4904 VAL
Chi-restraints excluded: chain B residue 4909 LEU
Chi-restraints excluded: chain B residue 4921 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0670
   chunk 18 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A4907 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.105652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.072915 restraints weight = 43665.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 5.38
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  10291  Z= 0.180
  Angle     :  0.976  16.718  14282  Z= 0.405
  Chirality :  0.052   0.442   1897
  Planarity :  0.005   0.089   1605
  Dihedral  : 14.112 113.436   3620
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.73 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.26), residues: 1076
  helix:  2.04 (0.67), residues: 73
  sheet:  0.72 (0.36), residues: 199
  loop : -1.73 (0.22), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B4804 
 TYR   0.013   0.001   TYR B4388 
 PHE   0.032   0.001   PHE A4854 
 TRP   0.037   0.002   TRP B4376 
 HIS   0.004   0.001   HIS B4704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (10108)
  covalent geometry    : angle       0.89687 (13793)
  SS BOND              : bond        0.00461 (   60)
  SS BOND              : angle       1.57303 (  120)
  hydrogen bonds       : bond        0.03085 (  198)
  hydrogen bonds       : angle       5.93316 (  501)
  link_ALPHA1-3        : bond        0.01234 (   11)
  link_ALPHA1-3        : angle       2.43534 (   33)
  link_ALPHA1-6        : bond        0.01130 (   10)
  link_ALPHA1-6        : angle       2.02590 (   30)
  link_BETA1-2         : bond        0.00821 (   19)
  link_BETA1-2         : angle       1.69382 (   57)
  link_BETA1-4         : bond        0.00773 (   55)
  link_BETA1-4         : angle       2.39853 (  165)
  link_BETA1-6         : bond        0.00783 (   12)
  link_BETA1-6         : angle       1.65588 (   36)
  link_NAG-ASN         : bond        0.00902 (   16)
  link_NAG-ASN         : angle       3.78874 (   48)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2670.00 seconds
wall clock time: 46 minutes 41.80 seconds (2801.80 seconds total)